By RAW there is no way to answer this for sure, magic missile does say it generates multiple missiles but this seems to be flavour rather than mechanical.
The key part I'm relying on in this answer is in the description of toppling spell: your force spell [snip] If the target takes damage
This clearly says that if the spell deals damage to the target then you get a trip attempt. It does not say anything about damaging the target multiple times, it just says that if the spell deals damage.
Based on this part of the rules the way I've been using the spell is to say that you get trip attempt against each target struck by the spell that you deal damage to no matter how many missiles you hit that target with. If you hit three targets you get three trip attempts (one on each). If you hit one target three times you get a single trip attempt.
I'm aware of the sneak attack/rays FAQ but it's speaking about a completely different ability and a completely different style of spell so I do not see how it applies.