Shortly before I died I encountered a group of big abominations in noer on the normal streets attacking me. do they take over the city on a higher world difficulty level? do they destroy it and kill the people and the humans because the game took already so long or is it just a bug?

Looking at this wiki, it mentions

After escaping, the next time Lona enters any location, she will be surrounded by flesh, you need to have enough stamina to escape, otherwise you will be returned to slavery again.

That might explain your encounter if it was the first since you had escaped them?