are you using room inheritance.. its always been a problem for me
Nope, but I do Duplicate rooms, room layers, objects, and sprites a lot.
I fixed my corruption issues by re-importing a few sprites that I had recently edited within GMS2 sprite editor.
So I guess in future it's safer for me to just create sprite assets in an external pixel art program as to not upset GMS2 with too much editing. I love the sprite editor within GMS2 too much, but if it means things will work better, I'll use something else for making sprites for now until the engine is more stable. :)