I got this reply from Rob on this since I found a lot of bugzillas on this one:
"This problem occurs when your project is using a facet version (web 2.5) but your descriptor clearly declares a separate version (web 2.4).
This has usually been declared by wtp as a project error and not a tools error. Obviously it's also a tools error but the logic in their code that recognizes project type is very complicated and I don't think anyone was ever able to fix it."
Can you check if there is a discrepency between your facet version and your descriptor ?
Then if you are really using web 2.5 then update your descriptor (I assume Rob meant web.xml btw.) to use web 2.5 and not 2.4 ?