I'm having similar problems with Booleans Difference.
When I try to cut a cross out of a flat plane it does one of the two things highlighted in the attached screen-grabs.
I need to accurately cut a series of crosses into this shape so that becomes akin to a perforated mesh.
The additional problem is that when I hit smooth (key 3) the shape distorts as does the accurate holes I'm trying to cut.
Can you help,
John