The only way I can illustrate this bug is by this example.
01 - Throw two clips (in my case two MOV-files) in Shotcut and move them to the timeline.
02 - Make a transition by moving the second clip over the first.
03 - Create a new track
04 - Move the three parts (clip1, the transition, clip 2) to exactly the same timeplace on the new track.
05 - Delete the track you were working on.
06 - Save the .mlt file
07 - Close Shotcut.
08 - Open Shotcut.
09 - Open the .mlt file you just created.
10 - (Try to) play it.