If you use more than one database in project plugin delete all files assigned to other than main database. IMHO: it's not a bug but dangerous feature ;)

eg. database_connection_A modelA -> file

database_connection_B modelB->file

plugin can't find modelB->id in system_files (model data is stored in database_connection_B) and delete file & system_files data record.

Maybe scanning/database.php 'connections' will be good idea?