Yes, I've noticed that too, but if it bothers you a lot, there is a "solution". Go to the bank and deposit the item that you put in the slot, then withdraw it.
Which reminds me... I bought 2 stacks of health potions, and I equipped one stack to a hotbar slot and used one, now one stack has 19 and the other has 20, and I find out, I can't actually equip the full stack to another slot, it will always have me equip the smaller stack.
So now I have 3 copies of the same stack of potions in my hotbar, and cannot access the other stack quickly.
Personally, I believe that should be fixed as well. If I'm going to spend the inventory slot, I think I should be allowed to use the potions quickly, in case my first stack runs out. Now I have to go through my inventory and quickly use a potion, now requiring several more clicks, and that's a hassle in combat.