I believe you are using an older version of builder plugin with GMS2.3.x - I have a fork with some additional safety checks (that I haven’t pull-requested back yet) on GitHub.
Downloaded new beta and deleted all my configuration files, created a new project just to test it and it happens still.
I believe it stops happening after you compile, but it seems fairly random, only thing that is consistant is that after it stops happening on an instance of gmedit it stops forever on that instance.