A method of avoiding around the problem is to open+close your inventory after each change to a hotkey that contains more than one stack of items with more than one ‘charge’, there’s some weird stuff going on with them currently.
I’m guessing it somehow skips a reassignment step, as every time I eat some chips or drink some water when I have more than one bag of chips or more than one bottle of water, the (1) charge item falls into miscellaneous and takes the ‘a’ key, then reassigns the next time I open any screen that links to the inventory, if you do anything that changes the inventory layout during this stage, there’s a chance it assigns the wrong key.