If they didn't put all the bolts back on where did they go? Did they chuck em over their shoulder or do they have a big bucket of unused bolts in the workshop?
But seriously, I would be checking the plastic undertray for your missing bolts. I know that I always drop at least one of them down there and it's a bitch to get them out. Maybe they didn't bother and just left them there to rattle about and eventually fall onto the road.