I’ve been having this problem for the last few months, not sure when exactly did it start.
Basically every time I open a pop up window (outline, replace color, frame/layer properties, etc.) the window becomes slightly larger each time, until eventually it covers the entire screen. And because I keep using these features constantly, I end up having to manually resize them back every few minutes of work.
Here’s an example of how it looks:
I have a 2 monitor setup, and mainly work on the main monitor split into aseprite (left) and any reference window (right); not sure if this helps but thought I’d share just in case.