Here's a video with me showing how it happens:
Disabling the last experimental option "Use native clipboard" didn't help
Updating Aseprite from 1.3.16.1 to 1.3.17.2 didn't solve it
It SEEMS like after the glitch happens (shortly after creating a new layer and painting on it) it won't happen again on the same layer.
It never happens on the first layer of the file. Glad to help, you can hit me up on discord "wotapoof" if you want to try something on my pc
Edit: correction to the video, it doesn't have to collide with the previous layer, can happen anywhere on the canvas