Last February, the entire U.S. F-22 fleet was grounded when it was discovered that inadequate (and previously undetected) drainage in the cockpit had led to rust forming on components of the ejection seat. The problem was quickly fixed, and the F-22s returned to flight status.
This sort of thing, rust in an unexpected place, is typical of new weapons systems. While the growth of more powerful design and simulation software has greatly reduced situations like this, it still happens. The Department of Defense spends over $20 billion a year dealing with rust problems, and about a third of them are found to be preventable. One reason carrier aircraft cost so much more than similar models used only over land, is the additional rust-proofing required.