The most common glitch I noticed was "interaction markers" (glowy white mesh) appearing where there was actually nothing to interact with. Like there should be a poster there to rip down or a torch to light, but there's just nothing there. A minor annoyance I suppose, but if they don't fix that I'll poop my pants.
Caution - You are approaching the periphery shield of Vortex Four
Connor is an assassin, it's mandatory that he has his hood on for anonymity. Besides I hate looking at his awful mohawk'esque haircut.
The chase missions are the worst. Don't push people, stay within X meters, attaching to unwanted environment, gold throwing runners, waves of enemies standing guard that can only be avoided with questionable area of effect smoke bombs, being knocked down and failing a chase sequence. Also if an informant spawns, you're close to him, guards are close, instant harass from the entire cities guards.
Almost forgot, you NEED the smoke bombs for the last chase sequence. Not equipped? Hold R2 to equip. Rinse & repeat until you pass it, extremely annoying.
You can force a jump with R1 and X to sort of scrape by a guard during a chase sequence, this staggers them and stops that annoying ghost hit after you pass them. I used this, forgot about smoke bombs almost the whole game, but that's how I got past the chase sequences.