I saw this mentioned elsewhere but couldn't find it. After loading up a game, some new items will not stack with your previous ones. I'll try to list the ones I've had issues with, think they are mostly potions. I've experienced this with a couple different items. Just happened with: Healing Potion. Edit: This also looks to only happen when the one on the save is in your item bar.
I had this happen quite a few times actually however I just place it all on the ground and suddenly some of them stacked, then after awhile of auto sorting they eventually all stacked again. No clue what's going on with that.
add infermal to that list More interestingly I could stack them to 3 one moment, then after some playing around just one, then after some more fiddling it got stuck to 1. I'm thinking of flogging this one I've got to try to 'reset' the problem
I'm gonna try keeping all potions off my hotbar until it's fixed. I don't think they'll be similarly bugged when loading back in that way.