I ran into this making a cross section of a complex object (see http://tcmacforum.imsisupport.com/index.php?topic=2199.0
for details) - "Two or more vertices of one body mapped to a single entity of other body".
In this case the fix was to rotate the object a few degrees - enough to move the vertices off the sectioning plane.
I've run into other ACIS errors in the past; this is the first one that I've ever understood well enough to get past. Hope this will help someone else who runs into this!