"Minimum percentage watched" is not respected whilst syncing watched history for some streaming services, e.g. Amazon Prime.
This is not a bug for Universal Trakt Scrobbler, but rather missing information from the streaming service.
When looking at the watch history on my Amazon account I can see that Amazon adds a play to the watched history immediately when starting playback of something. As far as I can tell there is no setting or information on the Amazon account regarding playback percentage.