Thank you for your post.
I am unable to replicate the issue with FileMaker Pro Advanced 14.0.5 (and FileMaker Pro 15) under Mac OS X 10.10.5. This is the same configuration as your crash report. This is what I did:
1. I created a database file with one Text field, "Name", and entered one record with the value "TSGal".
2. In Layout Mode, I increased the height of the Header part, and inserted into the Header a Popover button.
3. In the Popover, I inserted the Name field. I sized the Popover so its height remains within the Header part.
4. I created a script, "Close Script", with the script step:
Go to Layout [ "Table" ]
5. In File Options, I enabled the script trigger "OnLastWindowClose" to execute "Close Script".
6. I then close the file without any crash.
Let me know what I am doing differently than you so I can replicate the crash.