From the footage upthread, you can see that there was second bottle that rolled down after Thomas hit the first.
Seems likely it was the jolting from the raised cobbles section that led to the jettisoning. Which raises the question why, given how often riders have to dodge errant bottles, and given the peloton's presumed concerns about rider safety:
- Riders don't stop recklessly chucking them around with the wild abandon so many of them seem rather fond of
- The teams don't use bottle cages with better retaining capabilities, given how dire many road surfaces are
- The UCI doesn't impose better rules around bottle disposal (or enforce better if existing rules are actually adequate)
It always irks when I see them chucking bottles around the way they do, especially how regularly they end up rolling around dangerously among riders' wheels, or disappearing into undergrowth or remote areas from which they are unlikely to be retrieved. The only time it doesn't irk is when the rider does a gentle, well-aimed and well-judged throw to spectators.
The whole peloton and entourage should be directed to practise far more discipline in this area.