I reproduced this, and it is a bug that was introduced in v19.09 as a side effect of a bug related to needing to fix the filters on the second clip in the transition after you split it. Most people have the transition flow into the same clip that is the second part of the transition, and the bug is that it assumes this. This bug occurs with the following combination specifically:
- have at least one filter on the second clip in a transition
- put a different clip (or sub-clip) after the transition than what appears as the second clip in the transition
- split the clip following the transition
Shotcut is trying to move further away from transitions as being very independent clips and towards being managed as belonging to the clips before and afterwards. However, I think I can add a check that what is being split is the same as what is in the transition.
Update: Until the bug is fixed, I recommend you change your workflow to avoid splitting the clip following the transition. Rather, you can move the clip to V2, trim it, and then move it back to V1. Alternatively, before you add the clip that you were splitting to the timeline, while it is open in the Source player, trim it before adding it to the timeline.