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Probably a simple and quite noobish question, but I seriously feel like I've messed up at some point.

I am not too far into the game (hour or two), and I find exploring the city really troublesome after all the thugs in the city started attacking me. They didn't do so at first, as far as I can tell, and I have no idea what is causing it. It is seriously hurting my enjoyment, although after recruiting an ally they have become less of a chore.

I have tried walking around with my weapons unequiped and things like that, but to no avail.

Is this normal?
They tend to attack you quite frequently, yes. Especially if you stand around them too much. If you don't want to fight them you can usually just run away.
It's normal, they attack randomly. And yes it can be boring even if they quickly become very weak compared to your team... Avoid getting too near generic thugs - they have nothing to say anyway and ofter won't attack if you stay away, and you can usually just run away by changing screen.

Enjoy your playthough :).
Thanks for the answers!

Now I am torn between fighting them and running away, since running seems to aggro the other thugs easily. Then I have a cluster of them near the transit points between maps... Oh well, such is life on Sigil I suppose.
In my experience, they more or less reset or at least return to their spawning locations when you change map. Don't worry about having to face a bazillion of them when you zone in the next time :)
They attack you because thugs are thugs and they don't like your face. They are pretty weak though, even the zombies in the mortuary put up more of a fight. If you don't want to fight a big batch of them at once, let Morte insult them one by one to kill them seperately before they all spot you.