This is actually fairly common. There is even a [website dedicated to them][1]. 

Often this is a sign that the river is older than the mountain. They are often called **ancestral rivers and gaps** (such as the water gap and wind gap in the US). the river keeps cutting as the mountain rises (or the rest of the land erodes away) cutting a valley in it. The river does not even have to be older it just has to find a crack, or porous section to cut through. The trellis type of river drainage is known for having lots of such cross cuts. 

Also keep in mind flat areas may not have always been flat, glacier dams can redirect water AND carve flat land at the same time sometimes even push up smaller mountains and hills (moraine) from dropped debris which then get cut though.  


  [1]: http://www.durangobill.com/AncestralRivers/AncestralRiversIndex.html