I would suspect the crew would delete any duplicate points before they depart when checking the FMS route/SID/STAR. I know I do on my flight sim. Sometimes have the same problem, would have thought real aircraft would be a bit more sophisticated than my P3D and know what duplicate points are possible on the Transisitins/STARS/APPROACHES.
Alternatively, knowing this possible glitch after studying the app charts, maybe just don't pick the transition as the approach goes over that point anyway?