Sometimes Monodevelop and Unity can get out of sync and lead to frustrating issues such as clicking an error and not being taken to the actual line the error refers to, or double clicking a script to open the .sln in MonoDevelop and it opens just the script.
The best fix is to move the MonoDevelop.app package. It lives inside the directory Unity/MonoDevelop/, but if you move it one level out so you get Unity/Monodevelop.app, this should fix the issue when you restart Unity.
This simple fix saved me a huge headache. It comes from the Unity forums where there are a good number of other suggested fixes (here: http://forum.unity3d.com/threads/210405-Unity-4-3-how-do-you-associate-Monodevelop-with-the-Unity-project-Sync-doesn-t-work)