Usually that happens when the skimmer is not primed correctly and there are still air bubbles inside the plumbing that may be creating a partial obstacle and causing the water to backup. Try to prime the skimmer again and make sure that you remove the silencer when you prime the skimmer.
The other thing you can do is to rotate the return elbow 45 degrees to lower the water level inside the skimmer. The return elbow is the elbow located on the second compartment where the water goes into and makes its way back to the main tank. This elbow is usually installed pointing straight up but it can be rotated either side.