2004 S2000 Dealership Issues

2004 Honda S2000, 2.2L 4-Cyl, ~37k miles.

I have a Vortech Supercharger on my car. The dealership recently did some work to the clutch and in order to get to the clutch, the supercharger must be removed and the engine lowered slightly. The day after I got it back I noticed a strange whining. I then noticed three other things.

1. One of the SC mounting bolts was completely loose.
2. One of the coolant hoses to the aftercooler was loose.
3. The air intake to the SC was not fully sealed around the lip of the air filter, leaving a large gap.

There are two screws inside my air box now that were getting sucked up by the SC and destroying it.

Finally, my question. Is it too far fetched to conceive that the screws could have been sucked in through the gap in the air filter hose? The mechanic claims to have never removed the air filter, but he did remove the hose.

Thanks.