I have been having the same problem.
Canteen gives three charges(I believe it breaks once the charges are 3/3 {It is what happened to me}) Could be wrong here and kinda does not make sense to indicate depletion by counting up but whatever. Anyway,
I can fill the canteen but i cannot equip it in pocket slots to use by pressing F. Canteen not for drinking from?
P.S. I may have given my canteen away to an NPC.
Male, wears yellow-greenish jacket. No hat, no glasses.
@SirGreenDay
Have you tried drinking from the canteen without having Filtered Water in your inventory?