I believe the bottle was being refilled every time.
The bottle containing the correct potion is the smallest of the bottles in line:
“Got it,” she said. “The smallest bottle will get us through the black fire – towards the Stone.”
Harry looked at the tiny bottle.
“There’s only enough there for one of us,” he said. “That’s hardly one swallow.”
— Philosopher’s Stone, chapter 16 (Through the Trapdoor)
I believe this is a deliberate design feature: it means only one person can enter the final chamber at a time. If it was a group of people moving through the chambers, this would slow them down.1 Two of the other traps – the flying keys and the chessboard – reset after Quirrell went through, so it’s reasonable to suppose that it could happen here as well.
Why would you want it to reset? So that the first person through can’t stop everybody else.
If Quirrell just poured out the remaining contents of the bottle (or drank it in one go), then Harry is scuppered. I’d expect Quirrell to do this, so the fact that there’s any potion left at all seems like a pretty strong hint that these potions are not quite what they seem.