The hotkey link goes to the first item of that type in your inventory. IE it grabs the leftmost bottle.

Either swap the bottles so the full one is to the right of the empty, or drag the empty onto your hands manually.

What Felix said is relevant, I can confirm that. It's a minor bug and I think the devs would focus on bigger issues for now?

Yes, only fill the first in your inventory.

I had two plastic water bottles and two cantines that I wanted to refill at a water well somewhere.

All four items properly linked to the 1-0 shortcut menu on screen. I could only refill the one plastic water bottle and the one cantine, the secondary items was impossible to refill even if I held them in my hands.

I had to put the two filled water containers on the ground beside me, and then repeat the whole process of refilling the other water containers before picking up the two I left on the ground.

Read the first note, it'll save you some time in the future.

related to: http://feedback.dayzgame.com/view.php?id=3140 & http://feedback.dayzgame.com/view.php?id=3142 & http://feedback.dayzgame.com/view.php?id=717 & http://feedback.dayzgame.com/view.php?id=2937 & http://feedback.dayzgame.com/view.php?id=3140

What Felix sid didn't help me - even though I manually dragged empty flask to my hand I still ended up with a full one: they only swapped their palces in inventory.

i had to drop the full one on the ground in order to fill up the empty one.

Empty your hands then drag the empty one there.

What felix said, you have to baby sit the inventory right now, after filling one bottle, empty hands then drag new empty bottle in your hands, works all the time for me.

Felix this is a good solution to try. However, this trick only appears to be helpful for some, but not all. I have had this same issue, and I can say that I have tried manually dropping canteens into my hands. It always fills the same canteen. Even if I have removed everything from my hands and drag the empty canteen to my hands.

Duplicate of #9 (Hotbar (Using Non specific item)).

Please use the search function to check if an issue already exists before posting a new one.

Refer to the original to provide additional information on the issue.

Regards,
Johnny