I myself will not let a shop touch my wheels. Actually, I don't let them touch my bikes.
I've had too many similar experiences like yours. After learning to build my own wheels I see that "many" shop dudes don't really know what they're doing. Especially something like a tune up, they twist and turn but don't watch for binding spokes. I've gotten bikes back with popping sounds from the spokes, binding spokes. I've seen some shop workers true a wheel within 3 or 4 minutes, uhhh no!