Hi Defonten, that will happen if the object being booleaned is not a closed solid. When you select it, what does the object type indicator in the upper right corner of the window say, does it say "Solid" or "Joined srf" ? If it doesn't say solid then that's the problem.

The boolean commands are oriented around working with solids, they decide which pieces to keep and which to discard based on what volume they are contained inside of. If you don't have a closed solid which makes a volume then it will prevent that aspect of the booleans from working and it will function more like a surface trimming operation.

You can use the script from here to locate the open areas:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2

If you need more help could you post the 3DM model file of your object before doing the boolean so I could take a look at it?

Also you don't specifically say which command you are using, is it Boolean Difference or are you possibly using Edit > Trim instead?

- Michael