It is possible you may have found a bug I thought I had squashed. There is a counter in the room that measures enemies killed, then a trigger that releases the seed if you've defeated them all.
I ran into a similar (or the same) problem I thought I fixed - that if you defeat the last enemy IN that trigger (which is in the air) it doesn't count it properly. Something I'll need to iron out or rework in the near future. So cool you even watched a playthrough too :D
Sorry you were having troubles, but thanks for reporting the issue! Hope it works when you give it a replay!