Working for a non-profit can be great. If you are dedicated to the mission, it can give purpose to your work, which is key in being engaged in your job and feeling satisfied in life. In my years of working in HR, I worked for and with many different non-profits. While they all had their individual challenges, there were several common mistakes that I saw, regardless of size or mission.
1. Not staffing sufficiently to allow time off for employees. If your operation is significantly burdened when someone takes a vacation, you don't have enough people on staff. Burnout is very common in non-profits. If you don't allow your people to take a break, they will burn out much more quickly and will leave or worse - they will become disgruntled and stay.
2. Avoiding performance conversations. Because non-profits are often run by people with a tremendous compassion for people, performance conversations can be very difficult. When the conversations are avoided, co-workers or even managers get irritated and impatient with the under-performing employee, resulting in passive aggressive communication, which can often create a more stressful and difficult working environment for everyone. As I talked about here, leaders often believe that avoiding difficult conversations is compassionate. In reality, letting an employee know that they aren't meeting expectations, and then giving them an opportunity to improve is the compassionate thing to do.
3. Fostering and enabling an entitled environment. There is a phenomenon in non-profits where employees, believing that the mission is the end-all, be-all of the organization, will do things outside of their job descriptions, sometimes even in violation of policies, and believe that it is okay because they do it for the mission. For example, I worked with a manager who felt that she shouldn't be required to do payroll for her staff because she was spending time doing "more important" things, such as serving the needs of our clients. Another time, I had a staff member who felt that he could just not show up to a scheduled meeting with his manager because he was spending the time with a client. The bottom line is that in non-profits, just like in every organization, there are unpleasant tasks that need to be completed and unpleasant meetings to be attended. If the mundane things aren't attended to, not only could there be issues with compliance or audits, you will have employees choosing their own adventures day to day, with no consistent results or requirements being met.
4. Ignoring employee conflicts. Because non-profits are so mission based, often the day to day issues, such as employee conflicts are ignored. Can't they just get along? There is always something more important that comes up than dealing with two employees that are clashing. But when you ignore the signs of an employee conflict, the conflict will often boil over at an inopportune time. Talk to your people. Check in with them. Help them resolve conflicts as they happen, before it becomes toxic for them to come to work.
5. Assuming the mission is sufficient motivation. It's true that a lot of people will work for less pay/benefits if they are working for a non-profit in which they truly believe. That can only go so far, though. If you expect your employees to be devoted, pay them a decent wage (as you are able) and provide benefits if you can. If your employees are able to take care of their health and family outside of work, they will be more engaged in their jobs while they are at work.
Non-profits can be amazing places to work! Nurture your culture to be as meaningful as your mission.