Download the file called SmallBuilding_ExtrudeWallProblem.zip (7 MB) and extracted to your hard drive, and then double-click the HTML file to play the video in your browser.  

This video shows how to correct a support problem that I get occasionally in which extrude or other similar modifiers function in the wrong direction.  In the video it create and correct the problem in 3ds Max, but another potential source of the problem is 2-D geometry created on a UCS in CAD programs and imported into 3ds Max.  

Good luck and have fun
Ted