Random overrides in prefab instances

Hi.

I'm working on a mobile game with a few other developers and we constantly encounter a very annoying problem with random overrides in prefab instances.

By random overrides in prefab instances I mean that we have a group of "magical" prefab instances in our main scene that from time to time in certain situations get a override which breaks a lot of stuff.

By certain situations I mean that as far as we can see those overrides happen when someone is pulling new changes from repository (we are using git as vcs). We are working on both PCs and Macs and it seems that pulling changes from PC on Mac breaks a lot more stuff than when pulling from one PC to another.

Number of random overrides seems to be increasing week by week and we are basically drowning in bugs caused by overrides when we are trying to create a reliable build for iOS on a Mac computer.

We are losing a lot of time fixing those overrides and we have no clue how to even reproduce them, right now we are clueless. Have anybody had a situation similar to this one? Any tip would be really helpful.

We are using Unity 2019.1.5f