Hi,
Just simple and with few words, my suggestion is to disable Buffs for buildings that currently upgrading !
Some people didn't know that upgrading buildings is in pause mode when its upgrading, or sometimes people mistakenly buff a building that currently upgrading, I think its logically to disable buffs on it until that upgrading is done, at least for building that going from level 3 to 4 that need 1 day or buildings that going from level 4 to 5 that need 1 week to finish !