I found a solution and thanks to @Chip01 for bring me on the right track.

It was actually a "corrupted saved window size". With this information, I did some research and found the solution.

I just needed to rebuild the projects .idea/workspace.xml. The easiest and safest way was by closing the IDE (make sure that it is actually closed, especially on Mac), renaming the workspace.xml to workspace.bak.xml (or whatever name you like, but make sure to have a backup of that file) and restarting the IDE. After that, the popup window size fit it contents.