You can filter your library duplicates – this way you can identify movies that got mixed up with another existing item in your library. There’s no way for Plex to know if it did a wrong assignment (or else it wouldn’t have matched the movie in the first place).
If you’re adding items over time it can help to sort the library by “date added” for suspicious items. However if you just added all those 3000 movies at once, that’s not going to help. For that particular caveat you might want to rely on some 3rd party tools. There’s e.g. WebTools-NG with its “ExportTools-NG” component. This will allow you to export data from your library to a CSV or Excel format – the file will contain the items in a library but also the associated file names. So you can use it to look for the missing file and to see as what it’s been matched.
