I have finished "taking care of business" but when I walk into Ragged Flagon Cistern, Brynjof attack me.

Has anyone found a workarounds for this bug?

Did you attack/kill/steal from a TG member?

I am unsure, but maybe. This there a way to reset this?

You may have to start from an eariler save or a glitch.

I once walked into honeyside in Riftin and my housecarl attacked me. Gues she was happy to see me. I quickly exited and then walked back in "A pleasure to see you my thane" she greeted me like nothing was wrong

This is hilarious!
She could be putting on an act though, she'll slit your throat when you're nice and snug in bed.

She's probably got a cat somewhere far in her family tree. If they get way too excited, they can attack you for apparently no reason at all until they've vented most of their excitement. I advice you to return to her more frequently, so it won't build up like that in her anymore. ^^

Sometimes if you engage a hostile NPC and then 'sheath' your weapon(s) they'll reset.

I read another bug wherein Brynjolf attacks and the fix for that was to attack him until he takes a knee then when you heal him to full health he acts normal. Save first!

I restarted a new games and went right to Riften and still got attack So I deselected all Mods and it work

So it was a mod not sure which one.

Weird. ...good that it worked, but weird.