I think I had the same problem as you. My web.xml had version 2.5 while the project had the (right-click on Project-> Properties-> Project Facets->) Dynamic Web Module 2.3.
Although I tried to change the version from 2.3 to 2.5 ECLIPSE did not permit it. Solution: I removed the check mark under the heading Dynamic Web Module, I saved and I had Update Project. Automatically re-awakening is entering the box with the correct version. I use Eclipse Kepler.
p.s.: look at the comments of Jonathan just below, very useful.