I've just noticed the exact same thing on my March '07 CR-V EX-L, which has less than 40000 Km on it. (24000 miles) Rust is bubbling through the paint on the left hand side of the tailgate just under the chrome trim above the licence plate. GRRRRR!!!!I have a March 2008 CRV with exactly the same problem; rust spots on all four steel wheels! It's done just under 11k. Worse yet, I've just noted a couple of tiny rust bubbles pushing up the paint on the tailgate!!!
I called the dealer & they seem to be aware of this problem & they said it will be covered under the 3-year surface & 5-year perforation warranty, and I'll be calling their bodyshop tomorrow bright & early to book it in, but GRRRRR!!!! all the same. I have owned nothing but Honda's since 1984, one for as long as 7 years, and I have never had any rust issues before - and I live in salty, slushy Ontario. Colour me Not Impressed.