Wild swings in quality at low level management. I have known managers that are amazing, and I have known some that would make me walk away from the business rather than work for the individual. Some departments within the same store can be run very smoothly, with great emphasis on ethics and leadership, while others are estranging both customers and staff. Some managers are downright immoral, dishonest, and childish; and 2nd chance policies - while laudable - can make it feel like it is impossible to address or change such practices.
It can be VERY hard to get full time positions. Almost nobody gets fired from a full time positions (I've seen individuals written up for serious violations several times and still get priority on hours because of their "full time" status). I have even been told they are not allowed to hire or give out new full-time positions. I'm not sure if this is policy or just practiced by select managers. (As I mentioned before, some of the managers are incredibly shady - and from several conversations I had there was evidence that some of this was individual's way of manipulating their numbers to make their performance look better, not necessarily something encouraged by the company).
Hours can be very unstable at "part time" status (which most employees are). One week you'll be scheduled six days, be asked to come in early and stay late and have overtime, the next you'll have to bully someone else out of a shift to get 20hrs.
Strange inter-company emphasis about certain viewpoints. Can come off as cult-like in mentality and effort to push certain ideas onto their employees. Always struck me as relatively harmless (You don't have to OPENLY agree with their propaganda and often it won't be brought up other than inter-company publications, so it's not as bad as other companies I've worked for) but still subtly insulting to the intelligence and capability of their employees.