If you apply a transition to a junction between two clips on the same track in Premiere Pro, each clip is extended to generate an overlap covering the period of the transition. As a result, if you have applied the transition near a scene change, it is likely that the scene change will re-appear part-way through the transition.
Either leave enough 'room' for the transition, or move the incoming clip to a higher track and apply the transition only to the upper clip with manually-applied overlap, or double click the transition on the timeline and examine the detail in the Effects Control window.
