It indeed sounds like your database got corrupted. Sorry about that; we try to write bulletproof code, but since we're working against the WebSQL/IndexedDB APIs, there's always the possibility that something goes wrong at that interface, the browser crashes, lightning strikes your computer, etc.
500 errors indicate an internal PouchDB error, so you're not supposed to recover from them. Probably the best way to protect against corruption like that is just to set up continual sync with a CouchDB server (kind of the point of PouchDB anyway). CouchDB is a full database implemented from top to bottom and is very robust – since it uses append-only database files, your database can never get corrupted. So if you use continuous sync, you can always delete the PouchDB database and recover from CouchDB.
That being said, if you could let us know which version of PouchDB you're running, which browser you saw this on, or even a code snippet to reproduce, that would be really helpful. If you're using Firefox, you can also send us the storage files themselves for IDB by following the instructions here to find the Profile folder and then sending us the contents of the storage/persistent/<my_site>/idb
folder. Thanks!