I have a model with two parts and two mates. A simple pin with a shoulder in a hole:
The model has two configurations. The coincident mate has a different mate alignment in each configuration, which I am pretty sure is supposed to be impossible:
When I switch configurations, the model dutifully responds.
The alignment of the concentric mate is the same in both configurations:
The behavior becomes very unstable if you start making changes to the block dimensions or the hole locating dimensions.
These parts were originally in a real model with rebuild errors. I wonder how many other models have this problem that I don't know about.