I took a water bottle and tried to fill it up at a natural water spring on Sakhal. Filling up the bottle stops unprompted shortly after the animation starts even though i held the button. I had to try about ten times with different positions till it worked. Sometimes it filled up a little then stopped again.

Tried canteen and plastic bottles on 3-4 different springs. When you change the position of you character often enough you can find one where the bottle filling doesn't get interrupted. Best place i found so far is slightly outside the spring standing up.

To reproduce just try for yourself with a bottle on a spring several times.

No sudden and unprompted interruptions while filling up water bottles.