The fairy in the entrance room of the mansion after you fix it can take seeds of destiny you don't which causes an error that gives you 999 seeds if you go below zero. It will take seeds if you have them. Also I haven't been able to use any birth skill except the first on Leah.
I have also found some of the events that just say 'all characters need to be pregnant' even though I am maxed at 300/300/100 for the party. So the reason I can't use the birth skills might be because the game isn't considering my characters pregnant for whatever reason.
For more context I ran into these issues after doing the temple in the dessert.