HR/Benefits: I've heard a lot of employees complain about the benefits - but it's not that they aren't good; they're just really complicated. Unfortunately, there isn't a real HR department so getting information about that kind of stuff can be tough - and all the other cons that go along with not having an HR department.
Exec Leadership: While the exec leaders have done a great job hiring some very impressive people, it doesn't seem like they actually trust those people to do their jobs and/or recognize when talent "below" them have more expertise than they do in a particular area. They neither seek nor accept advice (at least sincerely), which frustrates those managers - and it trickles down to the rest of the company. There also seems to be no rhyme or reason with titles, promotions or organizational structure; and in an effort to get more accomplished, they pit employees against one another. It can be toxic, especially when they allow some senior managers bully their employees. And because there's no HR department, there's no where to air grievances or provide constructive criticism.