Where does a hex screw go

Had the ac checked and check engine light was on. Got the car back and found 2 unslotted black hex screws sitting in the area under the hood where the wipers are - they must have not replaced them. Also found
long rubber piece laying across the inside, maybe piece to keep water away from engine or something?

An you tell me where hex type screws are used on 99 vw beetle?

Thank you so much!