Macdale4,
As your friend said, this isn't "normal" but it happens. It's not a big problem and I don't think it will ever be an issue. Regardless of whether it's in warranty, it's a long way from a dealer to get the warranty and it will be your expense to get it there.
Since they said they wouldn't replace the roof and you said you weren't comfortable with it you could for your own piece of mind, fix it yourself. It's very simple.
I replaced a roof not too long ago and got a dry spot about 8 or 10 inches in dia. due to pulling the rubber back up trying to straighten a wrinkle. When it didn't stick back down I had to fix it.
You'll need to use water based roofing adhesive for EPDM rubber, as it will cure under the rubber. Any good rv dealer should give you an ounce or two. It won't take much. I used a syringe and plastic application needle about 1/8" in dia. A syringe from a pharmacy is cheap or maybe a turkey basting syringe.
It's a simple fix, clean a 1" spot on the bubble, take the syringe and applicator needle, shoot the bubble with enough adhesive to coat the entire surface that is loose. Squeeze it all around the bubble and back to the injection site, then suck the excess out with syringe. Put a dab of Dicor on the injection site. Your done, counting climbing up and down the ladder, about 5 minutes.
You said you had about 10 but unless they are larger, >4",I wouldn't mess with them.
Good luck,