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.