Chance of removing seeds from the ground before level 1 Foraging is 0 chance. Seeds are also harder to obtain from trees at a low foraging level. I haven't had a problem with tree seeds so maybe you are just having a tough time levelling up your foraging from the lack of trees on this small but very awesome and simple farm and so you should hit some trees in the forest bellow your farm and across the valley--in town, the mountain's, etc. I hope this helped your predicament.
I was already level 4 or 5 though, I'm not sure why it wasn't working. I had no smapi errors but I restarted the game anyways and that seemed to fix it. I have no idea what happened!
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edit: there seems to be something wrong with this map :( when you use any tools on the seeds on the ground to pick them up they get destroyed.