1. Management is often only slightly less clueless than you are about your career trajectory. My manager currently doesn't have a solid plan for what I'm doing 3 months from now, let alone 6 months or a year, which makes it difficult for me to plan my long-term career trajectory.
2. Lots of "policies" seem to be made out of thin air. I wanted to go to a conference a few months after I joined the team, and my manager (one of the original ~10 employees) approved it. Then, his manager (the CTO) rejected my request because there was an apparently unspoken, unwritten rule that new employees that have been with the company for less than 6 months don't get a paid conference attendance. I'm not upset that the policy exists, it's reasonable enough for a company that's trying to run lean, but the fact that not even my manager, who is one of the "inner circle", knew, made me feel kind of crappy about it.
3. Overwork. Everyone around me works 50+ hours a week. I try really hard to plan my week efficiently so that I stay at the office for exactly 40 hours per week, get my work done, and turn my damn phone off on the weekends. But one of my coworkers just had a baby and is still submitting code reviews at 1 in the morning. No one seems to mind that I am militant about my work-life balance, but lots of people around me seem to be getting burned out. One guy up and left for a couple weeks, and when he came back, he said he would only stay if they let him start working remotely full time. They approved his request, which is great, but it was the end result of 6 months of overwork and high expectations from everyone.
Now, let me be clear: I love my job. It's easily the most fun and stimulating job I've ever had, and thanks to my being adamant about my schedule it's not too stressful, but there are moments when I feel like I'm drowning a bit. Everyone around me is extremely sympathetic to each other, and we just instituted a make up time policy (if you have to work late due to emergency firefighting, you're entitled to that time back later in the week). We're also very open as a company about mental health and the legitimate need to take mental health days sometimes, which is extremely encouraging. I only hope that the dust begins to settle as the company continues to grow.