Why does the Nursery show seedlings that are already in the field?

Because their transplant isn’t checked off yet. Check it, and the Nursery shows your real tables again, with the room you really have left.

The Nursery follows your tasks: a planting is on your tables from its checked nursery sowing until its transplant is checked. Mark the transplant task as done in Tasks, or check Transplantation in the planting’s Quick actions in the Game Plan.

More in Keep your nursery up to date.