I modified a test cap from the original, and I think that it shows pretty clearly the odd behavior.
I simplified the situation: now there is no spawning, the contained sprites are already there, and it should be clear from the events that the arrow should point to the corresponding sprites, but they doesn't...
WTF. Even having one pair WITHOUT containers trigger this bug, but for each corrects it. Strange.
Also encountered two crashes, which of one I was unable to reproduce, and one happened when cloning a layout, and then copying the all events from layout 1's event sheet editor to layout 2's. I'll post it to the tracker.