When I first started with the company (over 5 years ago) there was very little communication between different teams and departments, which caused some duplicated efforts and misunderstandings/confusion at the time. Fortunately, they've gotten much better at communication since then, but from time to time things will still sometimes slip through the cracks.
For employees who work remotely, or from a satellite office, the health insurance is quite a bit more expensive. When I moved away from HQ, that was tough at first.
Also, there's this one specific button in the system that continues to taunt me with its very existence, despite my many attempts to get rid of it. (Though to be fair, that's more of a personal vendetta than a criticism of the whole company.)