...but only from the map!
Steps to reproduce:
1) Launch a ship that is at least 2 stages.
2) Stage away the first stage, continue to orbit.
3) Once in orbit, in map view, click the first stage that is still in flight but destined to crash.
4) Click the trash icon to delete it.
Not sure what of these is important, but that's what I did.
Hmm no just tried it twice with the same rocket and it did not happen.