For a level 3 upgrade to a city plan, your character should basically do nothing for 30-45 minutes, let all the scripts run. (look down at the ground, ENB off [Scr Lk])
There are not only all the scripts for placement going on and power/wiring, but the individual plots themselves.
If there are 20 settlers, that could mean 20 residentials, 20 work plots, and maybe up to 10 recreational plots. (yeah - 50 plots that need to be placed/upgraded).
If you try to refresh or watch a plot upgrade it can take a bit of time before it will complete its scripts and you get the notification.
Multiply that time by 50.
If you are doing other things, causing other scripts to fire, then it is possible that its just too many for the engine to handle and may be the cause of some CTD.