I went to a previous Save Game but the problem persisted. My problem began during the Muire D'yaeblen quest, which also appeared broken. I have the 1.31 update and this had never occurred before. Same thing happened to me recently while doing some Skellige quests. 'This may be a dead thread, but for the record. Walk around a bit and enter the inventory. You should now be semi-naked, save maybe for the bow. At the end, take all of your equipment off your body. The bow you might not be able to replace. Do this to every item and DO NOT exit the inventory screen.
That should put the item in your 'empty' slot and out of the empty slot will come out the equipment you already had on that was mistakenly marked as empty. Buy every type of equipment - chest piece, swords, bows, saddle bags, potions, and double click on them. Here are some messages from GOG forums that helped me solve this problem:
