Too many to list, but I'll try:
-- Poor, incompetent and unethical management -- there are some good executives, but they are in the minority. For example, we've took a $100M+ hit in the last 2-3 years that was solely the result of poor management and could have been completely avoided if the CEO didn't surround himself with yes men. But the CEO is more interested in being the "smartest guy in the room" rather than surrounding himself with the best and brightest. As a result, you get crappy executives or those that will just placate his ego rather than run the company well. Also the $100M+ hit in the Services org is only one of a few company-ending bombs. There are others. That is simply the only one that has been triggered thus far. I can't imagine this company surviving the next 12-18 months without being acquired (sort of shocked it hasn't happened yet) due to its precarious financial position.
--Lack of accountability in Management and in general. The CEO will say one thing and then completely reverse his statement 6 months later without acknowledgement of the change at all. Even when he's called out on it at a company meeting, he acts like he doesn't know what you're talking about. I don't know if that's just extreme duplicity or senility. Either way, it's a bad trait in a CEO. This same sort of Orwellian management style is seen in other orgs.
-- Irresponsible Decision Making. For whatever reason, management is more run like Game of Thrones than anything else. Instead of the execs agreeing on a course of action, you'll have different orgs doing clearly contradictory things. Eventually one org will win out, but then there is a loss of a lot of money and resources for the losing org. It's the stupidest thing I've seen. I don't understand why the CEO allows this to happen and why responsible decision making isn't possible. I suspect it's either because he's disconnected from the reality of what is actually happening at his company and believes the smoke that is blown up his backside or he's just too lazy or cowardly to really lead. He very much feels like an absentee father that says "go ask your mother" because he can't be bothered to be involved.
-- Culture of Fear. If you work under a good exec, you may not feel this. But if you don't, you feel it acutely. There is no accountability on the executive level. Bad execs (and there are several) blame their incompetency on their subordinates. So when something goes wrong, they place the blame on one of their VPs, Directors or Managers and he/she gets fired. This is their version of "solving the problem", but no changes are made into the process or policy that caused the problem in the first place. As a result, many employees spend a lot of time worried about others stabbing them in the back and engaging in CYA activities. It's exhausting and really hurts productivity and makes team work very difficult across orgs in particular. Some will admit that there is a lack of accountability/responsibility, but in the 5+ years I've been here, I've seen them do absolutely nothing about it. Execs stay, get their bonuses and stock, and the rest of us just keeping tolling.
-- No life/work balance if you're a high performer. For those of us that are high performers, we average less than a week off of work per year and many of us go without vacation at all for a year or two at a time. And now that we've switched to "unlimited vacation", we don't even get compensated for the vacation we can't take. If you're a good performer, expect to be working at least 60 hours per week to make up for all the other poor performers (and 80+ hours on a bad week). Good managers will totally recognize this as a problem (mine has), but they can't do anything about it because so many of our groups have been hit by layoffs. As a result those of us in SJ, generally leave pretty quickly (high turnover among high performers in SJ) because if you're going to be working those hours, you might as get the $100K+ in stock from a real company. Those poor guys in Petaluma are just stuck because who wants to commute 3+ hours each day.
-- No stock for non-execs anymore as a general rule. A couple of us are the exception, but it's very, very rare. The stock is only like $6/share so you aren't missing out on much money-wise, but it's definitely demoralizing. But, base salary is pretty competitive and bonus is so-so. They are generous with titles so if that's a big thing for you, you will get the Manager, Director or even VP title very easily -- but it's not the same as having one of those titles at a real company, so don't expect it to translate when you move.