I had similar troubles in eclipse and the only way to fix it for me was to
Just make sure you configure the web module before applying it as by default it will look for your web files in /WebContent/ and this is not what Maven project structure should be.
EDIT:
Here is a second way in case nothing else helps
org.eclipse.wst.common.project.facet.core.xml
, make backup, and remove the web module entry.