For me, this happens with Maven and Eclipse/STS whenever I update my IDE or import an existing Maven project. Go to the "Problems tab" (Window -> Show View -> Problems) and see what it says. Recently, the problems tab showed Project configuration is not up-to-date ... and suggested that I use Maven to update my project configuration, and this solved the "red X" problem. To do this, in the "Project Explorer" view, trigger the context menu and select Maven -> Update Project, as seen in this screenshot snippet:
