Hi,
Thanks for the feedback. This is probably because the code to know the number of affected rows of the delete MySQL query is not right after the MySQL query being run, but after the call to the onAfterFieldDelete event. And thus, if you have a plugin, like the action log plugin which does stuff in the database in that event, then it's possible that the wrong number of affected rows will be found, and if it's 0, then the error message will popup even if it has nothing to do with the real deletion of the custom field.
So I suppose that everything went fine in your case and you can just dismiss the error.
On our end, we'll change the order of things there so that it should not happen anymore with the next version of HikaShop.