I was about to finish my run then this happened and I have no clue about why. Could you tell me why this happened and how do I avoid that in my next runs?

As you can see in the video; when I get to that part of the city, those black squares start to appear. Can someone please help me overcome with this affair?

Also I run the game as administrator and I've already set the affinitiy to a single core. IDK what else i can do but I'm not doing anything that might trigger this.