User blog comment:Miskos3/Chapter 56, Review/@comment-17563801-20140409195724/@comment-7418318-20140411084730

If it had been Flegel, he would have had no reason to hide.

There are quite a few ways to explain how the MP knew. The most likely in my opinion is that they simply anticipated the possibility of Erwin & Co convincing Reebs to ally with them. Any doubt about this being true would have been erased when they found the blades on Eren and Historia.

Considering that Reebs already prevented the previous handing over, it's hardly a surprise if the MP had grown suspicious of him, even though he managed to make it look like an accident.