At times, the bar is set too low when it's hard to find a person for a particular position and teams are stuck with unproductive people.
Salary is below industry average, they try make up with bonuses and stock but it doesn't work. They only get away with this because people would accept a lower salary for open source work, but we miss on great employees because of it.
Hordes of new employees from proprietary software companies (Microsoft, IBM, etc..) couldn't care less about open source and culture changes internally because of it.
QA department quality is sub-par.
Engineering ladder has a rather low ceiling.
Office kitchens are not very stocked compared to other companies (silly, I know, I know..)