Thank you! I don't know why I never thought to look into the file itself. I deleted those lines and it's working again. The other duplicates you mentioned are fine, as they're connected just without a wire, but thanks for the worry on them. And I would report it, however I know I have an older version because I haven't been able to get a newer version running for some reason.

@thebusybee I have no idea what causes it. I just uploaded the file to here. It runs on Logisim Evolution 2.13.8. The "Register_Controller" circuit is the one with the issue.