sorry, but it really just seems like sloppy salesmanship and poor communication, not outright dishonesty. yes, the shop will try to make a profit off of you. that's what they do. yes, somes salespeople are less well-informed about some components than others. i have to look up a whole lot of prices. i could not tell you what a set of look keo pedals go for, much less anything related to dh mountain biking.
it sounds like the issue was resolved to the customer's satisfaction, yet the customer still complains. please go to another bike shop. they don't want your business.
shiahh.. i ahve never onserved the behaviour you decsribe. any wrench who takles parts off of an unsold bike and puts it on his own without paying for it would not have a job for long. besides, with distributors often offering employee discounts of as much as 30% off cost, there would be no real point to it.
the point that i was trying to make is that the salesmanm may have never intended to include the wheels in the reduced price and thought the customer understood that. this, in fact, seems to be the most likely explanation, despite the op's and skiahh's paranoia, bike shops are not in the business of alienating cistomers who drop $2500 in one day. they make their profit on service and accessories, and these require return visits.