One Trip Per Casting##Casting
The damage done by magic missile happens all at once, only triggering Toppling Spell a single time.
This is answered in the Pathfinder Core Rulebook FAQ in a question labelled, "Sneak Attack: Can I add sneak attack damage to simultaneous attacks from a spell? ":
No. For example, scorching ray fires simultaneous rays at one or more targets, and the extra damage is only added once to one ray, chosen by the caster when the spell is cast. Spell-based attacks which are not simultaneous, such as multiple attacks per round by a 8th-level druid using flame blade, may apply sneak attack damage to each attack so long as each attack qualifies for sneak attack (the target is denied its Dex bonus or the caster is flanking the target).