It appears that it actually only recognizes the "first" water bottle or canteen in your inventory (where "first" is the water bottle the furthest left in the highest container in your inventory).

Example: If you have a water bottle in your jeans and a water bottle in your backpack, you can only fill the water bottle in your jeans (because it is in a container 'above' the other one).

Example 2: If you have two water bottles in your jeans, you can only fill the left-most water bottle (because it is to the left of the other one).

My solution has been to fill the "first" bottle as normal, then move it such that it is secondary to the other bottle. For instance, I'll fill the bottle then move it to my backpack while I fill the one in my jeans. I have to do this several times if I have 3-4 water bottles or canteens.

Just in case it was helpful, I decided to time my most recent bout of unconsciousness. I have currently been out for about 74 minutes. I had been fairly well fed and drank a lot of purified water beforehand, so I'm sure it's just a bug!