If you continue from that earlier save the infamous random stuff at the Skyeline Appartments should never happen.

Why did it happen in the first place? What prevents it from happening again?

We don't know the technical reason, but experience has shown that long playing sessions will mess this map up and that shorter session will avoid it. It might be a memory leak or something similar that turns up if you play more than several hours in one go...

My first time into the skyline apartments all the door handles where replaced with two dart boards jutting sideways. In some of the apartments the ceiling fans where also dart boards, spinning and everything. Would have been great if I was a Malk.

I didn't reload, just went on with the game and when I had to return later (different play session - new quest), it had fixed itself.