AMP does not rename a source file when moving it to quarantine. It does rename the file placed into the quarantine folder with the .qrt extension. When a file is restored, the original name is restored. The only way I could potentially see this occurring is if the same file (matching hash) were quarantined on multiple machines in your environment under different names. If you believe this occurred and want to investigate further, please open a TAC case.
Thanks,
Matt