There are display problems with the wishing well, but I've always gotten any diamonds it said I was. I don't think this is something players can easily reproduce/confirm, so if you haven't already, you're probably better off filing an in-game bug report so the game mods can look at the logs for your city.
Right click anywhere in game and pick "Support" and you'll be taken to the page where you can create a ticket linked to your account. It wouldn't hurt to first copy the version at the bottom, and include that in the ticket.