Whenever I use the tools that are in the pickaxe slot and so on, it replaces the item in my hotbar and I get a visual glitch where I have one i the slot and one in the hotbar. When I then click on either it removes the visual glitch but the item that was in the hotbar is gone

I'm having this problem as well. It seems to be happening when playing on my server. I'm not sure if that is related. The most common time when this happens is when I'm holding down the left click. Typically in the case of instamining or when using my sword repeatedly attacking keeping the item active. The active tool belt item is moved to my hotbar deleting the item I'm currently holding.