You actually need to make sure you equip the bottle in your hand when you find the filling station then once you fill it, find the table and hold it out again where you put it.
Does the bottle disappear? When I click on it with the highlighted outline nothing seems to happen, cycling through my inventory doesn't seem to work either.
Edit: Okay, after looking through more comments I got the idea to check if the bottles were purchasable from the computer, they are. You need to buy an empty bottle first for 10$, then fill it, then place the bottle at the window. I thought the loop was to collect the empty bottle at the window, fill it, and then return it. Not the most clear mechanic so far.