I am really new to gamemaker, I am 1 month old, and I did not understand what you mean
OK, I may be wrong, but what I see is scaling.
What I see as an issue is somewhere in your game there is image scaling.
This may happen either in your object while drawing, in the rooms by view settings, maybe somewhere else, but I don't know.
What I do know is, that somewhere in your game something is crunching your graphics to a smaller size and that is where your pixel art changes.
I see 4x4 getting scaled into 2x2.
I may be completely wrong though, so if someone else have other ideas ease share.