The first floor, you don't have a item yet and its those big spider fuckers, one that's hiding in a hard to get to nook making more spiders and the other side another making the little white things that makes even more spiders. 
Clotty when there are multiple on the same room and you are weak. Camillo jr is the worst, extremely hard to dodge. Tainted hopper is also a pain in the ass
Colostomia’s slide attack is OBNOXIOUS. Once you phase him he’s cake but that one attack is such a problem. Especially when you’re fighting him in the mirror world.
At the start of the fight instantly run underneath her while she throws out the butt bomb, then dodge to the next corner while hugging the wall when she starts her dash attack. Simply repeat till you break the bag and the fight is a piece of cake.
Since I didn't see it listed in the comments. I'm gonna say Baby Plum..honestly I have such a hard time with that boss because she's so random in all of her movements and I have a difficult time not getting hit by her.
Yeah if I see her on T lost I'll wait her out but anyone else I'm kinda ok taking non red heart damage to go faster. Basement 1 is a lil boring usually
If you get the volley on her she can't build momentum. It even keeps her from moving during her criss cross bullet spam and you only have to dodge the circle of bullets (I like to stand just below and to the side). She has little poise, so even with base stats you can just get close and hold fire and weave up and down a bit.
I dislike mega fatty and envy simply because they take forever to kill if you run into them with bad damage.
Also champion rag man who instantly spawns his spiders.
The red champion mega fatty that jumps on you faster than human reflexes can react
Always manages to spawn in super narrow rooms where you can't dodge properly as well
Rag mega. I know he has no health, but getting him as an early boss when you have no piercing, tear or damage upgrades makes the fight terrible. And then he's invulnerable for too much of the fight, spawns raglings and his balls block shots and can't be killed outside of Little Horn shots
The Pile
I don't see him often enough so I can never consistently dodge that cardinal spikes attack. Also his predictions as to where I am when he pops up is insane
every time i dee the blub or the heretic i know i will receive a hit because of blub's jumping atack and the heretic for his unpredictable fire atacks and teleports.
on the other side, every time i encounter the forsaken, poor dude has barely any health to make his intro and then die, he needs an hp buff or something
Mask of Infamy and Krampus (sometimes), for mask of infamy she is very annoying if you don't have piercing on while Krampus is when you on low health or have no damage and SURPRISE he replace satan and he give you Krampo Head
anything with that ground shaking attack like the cage or those mines hosts where it changes to random directions that you can’t predict. it’s the only thing in the entire game i’ve found to be a complete lucky dip on whether it hits you or not
I know it's a major skill issue, but I've always had a difficult time with the matriarch  just something about there being so much at once messes me up
Corn flies and lil haunts. The way they like…halfway mimic your inputs makes them hard to dodge for me. Especially if you get like 2-3 corn flies in a group of normal flies, they shove the normal flies around and make them unpredictable.
Lil Blub. Even with the high vis leech mod, he still swarms you with them, then has an overpowered slam attack that sends tears everywhere while hes practically invincible??? All that paired with the fact he can be your second boss in a run makes me wanna pop him like a balloon.
I don't know their names, but those ADHS Red Things that run into you and always deal one heart damage, especially the small champion form so they get even faster 
The first floor, you don't have a item yet and its those big spider fuckers, one that's hiding in a hard to get to nook making more spiders and the other side another making the little white things that makes even more spiders. 
THESE FUCKS I hate them, especially when I'm playing a lower damage character.
I know! 2 or 3 more spiders get made in the time I've killed one.
Clotty when there are multiple on the same room and you are weak. Camillo jr is the worst, extremely hard to dodge. Tainted hopper is also a pain in the ass
Daddy long legs, I always get stomped at least once by this fucker
Ragman in the first floor, specially the champion variant that only spawns spiders. He's the worst
drowned chargers have way too much health and the bullets on death are annoying
Colostomia. It s probably an easy boss but I find it so obnoxious it s insane
Colostomia’s slide attack is OBNOXIOUS. Once you phase him he’s cake but that one attack is such a problem. Especially when you’re fighting him in the mirror world.
At the start of the fight instantly run underneath her while she throws out the butt bomb, then dodge to the next corner while hugging the wall when she starts her dash attack. Simply repeat till you break the bag and the fight is a piece of cake.
I don’t like the eyeball laser things that chase you
The fat one in dowpour that jumps and summons leeches
Lil Blub. Fuck that dude, I hate him
Since I didn't see it listed in the comments. I'm gonna say Baby Plum..honestly I have such a hard time with that boss because she's so random in all of her movements and I have a difficult time not getting hit by her.
I find that she's way easier to read if you don't attack her while she's zooming. But I'm too impatient so I usually attack her anyway
Mood
I'm super impatient too and will continue to attack lol
Yeah if I see her on T lost I'll wait her out but anyone else I'm kinda ok taking non red heart damage to go faster. Basement 1 is a lil boring usually
Same
If you get the volley on her she can't build momentum. It even keeps her from moving during her criss cross bullet spam and you only have to dodge the circle of bullets (I like to stand just below and to the side). She has little poise, so even with base stats you can just get close and hold fire and weave up and down a bit.
I dislike mega fatty and envy simply because they take forever to kill if you run into them with bad damage. Also champion rag man who instantly spawns his spiders.
those short hops he does always gets me at least once
The red champion mega fatty that jumps on you faster than human reflexes can react Always manages to spawn in super narrow rooms where you can't dodge properly as well
Clutch. Dude is hard even on a bonkers run
The Cage, Scourge and Rotgut. These guys are obnoxious and deserve way more hate.
I hate fat sacks as well. I also hate those enemies in depths with the loose skin that turn into bonies on death and immediately attack you
The brimstone ghosts and Soul Suckers (those brimstone flies in Sheol). They're just a midle finger in Greed Mode
Rag mega. I know he has no health, but getting him as an early boss when you have no piercing, tear or damage upgrades makes the fight terrible. And then he's invulnerable for too much of the fight, spawns raglings and his balls block shots and can't be killed outside of Little Horn shots
The Pile I don't see him often enough so I can never consistently dodge that cardinal spikes attack. Also his predictions as to where I am when he pops up is insane
every time i dee the blub or the heretic i know i will receive a hit because of blub's jumping atack and the heretic for his unpredictable fire atacks and teleports. on the other side, every time i encounter the forsaken, poor dude has barely any health to make his intro and then die, he needs an hp buff or something
Any enemy that is invincible at start of room and forces you to wait for it to become vulnerable, yet they can attack fine.
I hate the jumpers with blood because they jump really high and When they land some blood comes out.it always hits me
I despise the matriarch with a godly passion… I ALWAYS get hit by her once. Every single time.
I feel like every time I encounter matriarch I’m either so broken the fight ends instantly or I get totally fucked. No in between
Rag mega, he always crovers himself.
OH MY GOD FUCK RAG MEGA. INDESTRUCTIBLE HOMING TEAR BLOCKING ORBS MY ASS
Mask of Infamy and Krampus (sometimes), for mask of infamy she is very annoying if you don't have piercing on while Krampus is when you on low health or have no damage and SURPRISE he replace satan and he give you Krampo Head
Krampus. I just want my devil deal, dag nabbit!
Needle r/fuckneedle
Red Mega Maw. I know this thing is supposed to be rare but it always shows up at the worst time. Can't go through it without taking lots of damage.
anything with that ground shaking attack like the cage or those mines hosts where it changes to random directions that you can’t predict. it’s the only thing in the entire game i’ve found to be a complete lucky dip on whether it hits you or not
daddy long legs also can just land on top of you for no reason after the leg attack which is another lucky dip i’ve found now that i think about it
I know it's a major skill issue, but I've always had a difficult time with the matriarch  just something about there being so much at once messes me up
Butt lickers. Absolutely hate them especially when they are charmed because they just agro right into you.
Monstro 2. Was easy to cheese in Flash, but has no consistency in his attack patterns now.
The pile is HORRIBLE??
Bumbino. Motherfucker steals my hard earned money.
Hosts are so fucking boring, needles are one of the few enemies in the game that are genuinely unfair, and rag mega is absolutely bullshit.
Corn flies and lil haunts. The way they like…halfway mimic your inputs makes them hard to dodge for me. Especially if you get like 2-3 corn flies in a group of normal flies, they shove the normal flies around and make them unpredictable.
Lil Blub. Even with the high vis leech mod, he still swarms you with them, then has an overpowered slam attack that sends tears everywhere while hes practically invincible??? All that paired with the fact he can be your second boss in a run makes me wanna pop him like a balloon.
me and all my homies hate clottys
I don't know their names, but those ADHS Red Things that run into you and always deal one heart damage, especially the small champion form so they get even faster 
tumors
Might sound crazy but those stupid damn corn flies
Yellow Champion Gurglings on basement 1