Perhaps it's because they had different folder/file names?
Yes, that would be a known v23 issue: https://github.com/itchio/itch/issues/1244
itch v23 handles properly a chain of builds pushed with butler - old files are cleaned between upgrades, even if the game is shipped in subfolders that include the version number (a strategy we don't recommend, and that makes patching more expensive for no good reason).
However, when switching between uploads (not builds), itch wouldn't clean files from the previous upload that aren't in the new upload - the result is several copies of the game in the install folder, and there's a good chance it would launch an older version rather than the latest.
(If you're wondering how that bug slipped into a stable version of itch: it's a pretty rare scenario. Usually games are shipped without folders-with-version-numbers, which works fine (the newer files replace the older files). Also, usually wharf uploads stay up, and just get updated normally).
I'm happy to report that this won't be an issue anymore as of v25 - all the installing & upgrading logic has been rewritten from scratch, with better testing, and it cleans up in all possible cases. It's also stricter in what it considers an upgrade.
itch v25 is slated for release in the next few weeks, you can already test the beta here if you want: https://fasterthanlime.itch.io/install-kitch - it's at a point where it's usually more stable than v23. You can check out the complete roadmap here: https://github.com/itchio/itch/projects/1
v25 has been in the works for about a year now. I'm really looking forward to leaving v23's bugs behind.
I'll be looking forward to the public status page so that we can know if errors are happening on our end or not before a release, thank you.
I've deployed a status page here for the time being: https://status.itch.ovh/