My pump is mounted right next to the downtube bottle cage, kind of on the side of the bike. While I've never knocked the pump out of its housing, I have knocked it loose once or twice with my bottle.
It has two plastic "C" clips and both times I have knocked it out of the top one. One good bump or and it would have fallen out completely. If your pump is similarly mounted it's not inconcievable that the wind and your pedaling shook it loose.