The only thing that sounds off to me is the brake rub, however I have seen wheels that were bent untrue themselves to return to their equilibrium after being serviced. Also, mechanics are people and miss stuff. I know on a busy day I've taken a wheel off and put it back on, intending to, and believing I did, true it. When you build five bikes and do five tune ups in a day, while stopping and walking away from what you're doing repeatedly, to help customers you're bound to miss something. Of course, a good shop will look at the bike when they return it to you and correct issues, since they know it happens. On a busy day accessories get left on the bench all the time. Especially seat wedges. Since most work stands grip the seat post, it's often taken off to provide enough post to clamp safely.

I usually replace anything under about $10 that needs it without asking for approval. Cables, tubes, small runs of housing, it's been my experience most people are more interested in a functional bike than being bothered with an explanation of why I can't make it work as is. They're usually happy to pay the extra couple dollars and if they seem unsure I'll explain to them what and why I replaced, and that's it. You should receive quality service but don't expect people not to make mistakes from time to time.