I'm not very far along the bard's college quest line but I have been helping them. I play a good character so I haven't been stealing and I'm not sure if another quest
lead me to do something wrong but all of a sudden 3 thugs attacked and the contract said she sent them.... what?

Anyone know why this might have happened? I don't want my questlines to be messed up or anything ><

Maybe you accidentally opened up one of her drawers that said steal from you don't have to take anything just opening it will get thugs to come after you.

Yup, I stole from Alvor in Riverside and he sent three guys after me. They finally caught up to me in Dawnstar where they were left in snowy graves.

This surprised me the first time it happened. How the heck did they even know I stole, I was not spotted! It ticked me off really.

I stole from inn in whiterun for this guy, he wanted some mead or something, and then i leave not thinking anything about it since no one saw me. later three bruisers come to knock me around, when i found the note on one of their bodies i was genuinely shocked

also, i ran into a DB assassin trying to kill me, didnt say who took the hit out on me, just that someone did. i was being good too. maybe the family of a bandit i killed?

You were last in the room, the item went missing... how stupid are the NPCs supposed to be? (ok, don't answer that)

Anyway, I don't believe the thugs require forensic evidence before hunting you down, just "some cash and a name".

I stole some of Alvor's ingots by the worktable. No one could have known it was me, but they magically did

This doesn't mean you stole anything. Sometimes if an NPC gives you an item and you don't do the quest for a long time, they send thugs after you in case you stole the item. THe note they carry will say they're supposed to remind you of your obligation and to only use force if necessary. You can confront the NPC about it, if this is what happened.

The chickens, they're everywhere, spying on you. The real guards among the knee-damaged 'Guards'.

Damned chickens! Always these animal spies!

The horses are onto it also!

Fools! It's Detective Cluck and his band of Cluck Rangers, scouring the land for mischevious Dragonborns who commit petty theivery or outright murder.