Audacious 3.6.2, Ubuntu 16.04.1 LTS
In library some files (noticed only for flac for now) are duplicated. In folder one file for each song. Thought cue-files could be problem, not the case. OS indicates 3699 files, Audacious shows 3810.
Audacious 3.6 is ancient, please try the latest version. You can use the WebUpd8 PPA for example.