My list:
1) Re-orgs upon re-orgs believing they'll fix underlying problems
2) Related to 1), lack of accountability when it comes to decision making, like when no one is accountable for the previous, failed re-org when deciding to re-org again.
3) Spending way too much time trying to make perfect decisions, especially around product vision. Much better to decide quickly, be flexible going forward and iterate.
4) Providing perverse incentives. As an example, one place I managed didn't give lower-level managers a budget, only a headcount. So, of course, everyone hired only senior and above developers. This created logjams during promotion time and forced a lot of turnover which could have been avoided with a more balanced hiring plan that included more junior devs.
5) Seagull management, especially from the C-level. For those not familiar, it's swoop in, shit all over everything and then leave others to deal with the mess. Either provide minor course corrections or devote a significant portion of your attention to that area until it's stable.
6) Being too good of a motivator. This doesn't sound like it should be a problem, but I had one manager who was so good at selling shitty ideas to the team that we kept working on the wrong vision. A good vision should largely sell itself.
7) Not caring enough about their employees as people. When the difficult conversations need to be had, it's a lot easier to deal with it if there's an underlying relationship where the employees feel appreciated and considered. It doesn't mean you have to be their friend, just that they believe you care about them. The easiest way to make them believe that is to actually care about them.
8) Not devoting enough time and energy to hiring. This was my secret as a manager. I put a lot of time into recruiting (lots of after-hours meet-ups and mixers) and was picky with who I hired, built a great team, worked to keep them happy and focused and then spent 3 years getting awesome reviews for doing basically nothing but shielding them from unnecessary distractions.
9) Rewarding busy over good. Who deserves most organizational praise, the employee who valiantly wrestled with a production issue until 4am or the employee who pushed a non-event release to production and went home at 4pm? I'm amazed at how often managers recognize and reward the former when the latter is giving customers a better experience.
I could probably come up with another 20 or so, but these are the ones that have cropped up the most in my experience.