Cell Fracture addon leaving unfractured boxes? I have been trying to make a short clip of a bullet hitting a wine glass with wine in it, but I keep running into the same problem with the add-on. Every time I have used it the result has left me with at least a partial box being generated as several of the fractured pieces.

I have tried subdividing and/or adding a sub-surf modifier but the result only changes where the large distorted fragments end up. I have been having trouble with this for quite some time and I would greatly appreciate any help.
This is caused by a failed boolean operation.

The cell fracture uses the boolean modifier internally, if boolean fails because of geometry it can't handle (typically because of a non-manifold mesh), this happens.

Note that for 2.70 the boolean modifier has been upgraded to support ngons and a newer version of carve, so this will likely improve results in some cases, however there are limits to what boolean can operate on since it relies on calculating inside/outside of a mesh which can be problematic.