I'm assuming that the wrinkles you are seeing are not being caused by a edge being loose and the roofing material coming loose from that edge causing the wrinkling. My belief (and I've been told by my dealer) is that a few wrinkles are no big deal. However, my suggestion would be that you report the wrinkling as a possible problem. Let the dealer check it, and they will probably report that no problem was found. Make sure their report is listed on your receipt (which should be for $0); if a problem later develops with your roof, the receipt may help you with a potential roofing warranty issue.
There's lots of advice and information in forums... sometimes it is correct. For example, all of my posts are made by a political appointee who got the job as a reward for contributions to my diesel bill.
2011 Jayco 28.5RLS; 2008 Chevy Duramax; Pullrite Superglide Hitch