Sometimes the Boolean difference modifier produces tiny hard to see holes that may cause problem in later stages of modelling, particularly for the upcoming dynamic topology sculpting. This usually only occurs on meshes with non-trivial polycounts.

To reproduce:
1. Open attached example .blend
2. Apply the Boolean modifier on the selected object

The problem will not be immediately visible, so to see it better:

3. Enter edit mode
4. Select->Non-Manifold
5. Run a couple iterations of vertex smooth on the selected vertices to see the holes.

Tested on r51802, windows 64.