Lack of focus on quality: other people have mentioned this, but there is a real problem with quality at MITRE. Projects spin up, execute, and spin down in a period of months, and they are therefore built on extremely rickety foundations. This is dangerous, because the glue and baling wire holding things together aren't always visible from the outside, and engineers who have spent their entire careers at MITRE start to lose the ability to recognize quality issues at all.
Haphazard recognition and advancement : the people who make promotion and salary decisions are not the same people who see the work you do every day. Your advancement is often based off how glamorous or polically significant your work is, and not the actual quality of your work product.