In my opinion that is actually very understandable. Imagine if you were the POI and you had to choose a few students for your own lab, out of ~3000 students`. You will no doubt want to have a think about the choices you have made, and not disgard the student just because he/she has one particular thing you didn't like.
It is actually a good thing they don't reject students straight off the bat, and really look at each student carefully, think about them and choose according to their needs. You got to remember MIT is perhaps the only top school that does not look at GRE scores, which in many other schools use as a filter to weed out weak students. I like to think MIT is better than that.