I had a web app configured and running when I shut down my PC. Then when I started it strange things started to happen: I use eclipse indigo ee. It gave me a class not found
Apparently the environment is dirty. I'd suggest to clean and rebuild all.
It isn't possible to pinpoint a real cause for this problem, there are too many possible factors. For example, the workspace wasn't properly shutdown, or Tomcat wasn't properly shutdown, or you did "too many" things simultaneously which caused race conditions in background tasks of Eclipse, etcetera. This is not explicitly related to Eclipse+Tomcat combination. This happens to my experience also so now and then with JBoss AS and Glassfish servers.