Sims 3

@thenia  If you use mods or are willing to try a few, install NRaas MasterController, click on the sim, and select:

NRaas > MasterController > Basic > Sort Inventory

This not only sorts based on whatever criterion you choose but can unstick any currently stuck items.

If that doesn't help, can you separate some of the seeds from others?  Try to do so—specifically move them out of inventory and onto the ground.  Then for the rest, use MC to delete them.  Click on the ground of the lot and select:

NRaas > MC > Object Stats > Inventory

Find the seeds on the list, which will include only those in inventory (not the ones you moved to the ground), select them, and flush them.  For this command, you would need the MC Cheats add-on in addition to the base mod.

You could remove MasterController after you were done, although I'd keep it just to have its commands available.  MC doesn't do anything on its own; it only intervenes when you deliberately issue a command.

If you're not willing to use mods, and you have Generations installed, you could try giving the seeds to another sim.  Here again, remove the ones you'd like to keep using first.  But I'm not sure the other sim would accept the gift or that the seeds would actually transfer.

The only other suggestion I have is to evict the sim in Edit Town and put them back into their house.  I don't know for sure that it would help, but it can unstick items some of the time.