I fill skins from the inventory like this too, and have had some struggles in the past. I’ve found repositioning the view on the well can help, but not always.

An observation on the posted video…

The player is consuming the contents of the water skins while attempting to fill them AND when stepping away from the well, the water level is very low, as if the attempts to fill the skin is also consuming the water from the well.

Have no clue how/why this mechanic is messed up - but it is clearly not working correctly.