I had the exact same issue while working on a GIT based project. I was able to resolve by changing the way i was importing the project in the workspace.
Wrong way : Import project to workspace from GIT perspective , like right click on the GIT URL and selecting the option import which was not recognizing the project facets.
Right way (which resolved my issue): clone the project in GIT perspective , change to JEE Perspective , then import from file > import > Existing Maven Project .