Sometimes no matter what program you use, boolean union may not be possible and/or will cause artifacts or lost faces. This is especially true with cad programs when exporting the file out to stl. It is important that there are no faces occupying the same space (co-planer) or this will cause lines on the major surface parallel to the build platform.
Bring that model into PreForm and you should recieve an error. PreForm will attempt to crrect it. Scroll through your layers and you should see jittery layers, some may even have edges the act like hollows on the interior shape.