I have had this problem too. Very frustrating. I had the bizarre notion that maybe you need to have some connection to the area. For instance, my sim can harvest in her own surroundings and in the lot where she used to live but cannot in the other town or the other lot where she has never lived and knows nobody. I have had no trouble with the frogs or the rocks so maybe it is just a bug.
I have also found that the plants, grown at home do not die if they are looked after - not ever. I wonder if this is intended. Seems strange that they would not eventually die of old age.
By the way, totally unrelated, but I have had a plate of food sitting on the side walk near my sim's house for umpteen sim years and it never spoils.