I had the same issue with npcs popping up around me (or buildings in the distance missing walls, etc.) until I moved the game from my HDD to one of my SDDs. Don't believe that this should be an requirement to fix this issue but at least in my case the pop ups obviously had something to do with hard drive accessing times.
I would also like to add that I did not notice these issues in prior versions of the game. It was only after V1.03 was released that this started happening (but then again I won't place all the blame on the patch. Maybe I had simply not arrived in Novigrad before V1.03 hit. I never had problems in any other city but Novigrad)