The main one for me is how bad the benefits are, the health insurance is easily the worst I've ever had. Even with their "best" plan you'll still be paying $80+ out of pocket for routine doctor visits. I wish I had scrutinized this more closely when negotiating for salary.
Another problem is onboarding, while corporate has made a big effort to improve new hire onboarding the experience takes a dive once you get assigned to a program. Standards vary wildly between programs, they all have their own drawing sheet formats, PowerPoint templates, & so on that any outside experience you bring is likely to be irrelevant to completing actions. This is exacerbated by the long-term employees often refusing to take the time to teach new employees these program-specific quirks. The training offered is about 50% "you'll be taught more about this on your specific program", which is more often than not a lie.