I was really puzzled when landing at Milan Malpensa (on a Wizz Air flight from Budapest) we needed to go through a passport control. How come? I thought if you don't leave Schengen you don't need a passport control.
Due to the situation in Europe, many sovereign states have re-instituted immigration checks. Checks could possibly be performed randomly or continuously is some circumstances.
If you search on "suspend Schengen" or "Europe border controls", you will see numbers reports of this over the past months, particularly with respect to France, Italy, Austria and Denmark.