This seems to be a common issue on the 2000+ unfortunately, but doesn't occur on all these cars like the hood herpes does. My 03 has one very tiny bubble, a couple other cars I looked into buying had one as well. I know of at least one member who has several bubbles in the same spot too. But I know several 2000s – which are 7 years old now – that dont have any bubbles. I don't know exactly how they form, but I THINK it has something to do water being able to seep in between the metal from inside the gas door. It has to be rust forming underneath the paint. It has nothing to do with how your wife may take care of it.
I have to take care of mine ASAP so it'* easier to fix. I only hope it never returns.