The choices are hidden when you don't have the required fertilizer or seed, that's why you can't see the option to use it while you don't have any of the mineral fertilizer in your inventory.
Are you certain that you got it, and didn't use all you received already? It's the first time I hear about this issue. Maybe it was just a wrong text telling you that you got the mineral fertilizer, but it was actually one of the other types? Or did you got it several times?
You can you send me your save file per mail to Naughty-Netherpunch@web.de, if you think it's an on-going issue in your save. You can find your save files in the www/save folder. If you can send me the .rpgsave file with the save slot number in which you have the issue, I can check it. (Doesn't work if you're on android)