The recent PR dalehenrich/metacello-work#3 introduced the bug. Metacello/metacello#504 will patch the bug, but a better solution is to change the upgrade script to tolerate this situation, since closing a ZipArchive is a good idea.

This issue is recorded as internal GemStone bug 48168 - Recent Metacello update introduced a bug in 3.2.x upgrade to 3.5.0