I have two Strats, a 2005 American Standard SSS and a 2008 American Deluxe Mahogany HSS. And BOTH developed short (less than 1/2 inch) hairline cracks in the clear coat where the upper cutaway wood narrows and touches the neck at the corner. I thought it was a fluke combined with aging in my 2005 American Standard, until my newer 2008 American Deluxe developed the SAME crack in the exact SAME location during the very SAME time period. I finally chalked it up to changes in the weather, which where I live (MN), can be 70 degrees and humid one day and 20 degrees with very low humidity the next. Obviously, inside a house the extremes aren't as pronounced but they are there nonetheless. The guitars were merely sitting in their cases when one day I pulled them out to play and surprise... there are cracks looking back at me. I would maybe expect this on the Squires or MIM Fenders, but it is rather frustrating on the USA models which carry a large price tag. I doesn't matter from a playability standpoint, but if I want to resell, I can't really say they are in "mint" condition. I become more "OCD" with each hundred dollars I spend on an item. I think that is normal behavior. Short of going with a guitar with a Les Paul shape, I'm not sure how I could have prevented these cracks in the clear coat of my Strats.
It would be interesting to hear from people with Fender Highway One Strats to see if their non-clear-coat finishes avoid this malady.