I was on explore and I tried to pick up some wheat and it said "you don't have enough space in your inventory!" So I went to my inventory and destroyed some cuttlefish ink,then went back into explore and it wouldn't let me get the wheat,it let me get the surrounding wheat but not the piece I was on.

You need to leave the spot where your pet was standing and then return back to it. Picking up is triggered only whe you move to a tile. If this doesn't work, please try a hard refresh (refresh with clearing cache). 

If the piece that you can't pick up is NOT wheat and you tried to get it before wheat or any other new item and right after clearing the slot by destroying all your cuttlefish ink, then you reached the limit for this item  (9999 for food, 999 for everything else).