To reproduce:
1) Create a script with the following code. Note the Debug.Log is commented out.

```
using UnityEngine;
public class TestScript : MonoBehaviour {
void Start () {
// Debug.Log ("Start"); // breakpoint here
}
}
```

2) Place a breakpoint on the commented line. It will automatically move to the next line, that is expected. Attach MonoDevelop to the Editor.
3) Enter playmode in the Editor. The debugger will stop at the end of the Start function.
4) Press the continue button in MonoDevelop. Don't switch to Unity just yet.
5) Uncomment the commented line. Save your changes.
6) Switch back to Unity
7) Wait for script to recompile
8) Switch back to monodevelop
9) Place breakpoint on uncommented line
10) Switch back to Unity. Stop and play scene again
11) Notice that breakpoint isn't triggered
12) Try to place breakpoint on Start method. Circles with transparent middle part appears next to line and error is thrown.

Reproducible with 5.5.0f3, 5.5.0p1, 5.5.0p4
Not reproducible with 5.4.3p4, 5.6.0b3