I've used Playa on a large number of sites and haven't seen this issue, so I'm wondering if anyone has ever seen this before.
I just installed Playa on an existing site running EE 2.5.3 and using Playa 4.4.3. I've set up a Playa field to show results from a single channel and to only show results from two of the categories that are assigned to that channel. If an entry in the related channel is tagged with both of the categories then it shows up twice on the left side of the Playa field.
So in this instance, the Playa field is pulling in results from a Sponsors and Exhibitors channel. This channel has two categories so an entry can be marked as either a Sponsor, an Exhibitor, or both. If an entry is marked with both the Sponsor and Exhibitor category, then it shows up twice in the Playa field. If I remove one of the categories, then it shows up only once in the Playa field.