Check the file in Acrobat/ Illustrator and clean it up suitably. using the file directly wil lalmost certainly never work because CAD programs add a lot of data and create odd constructs with clipping masks and duplicate paths when outputting to PDF.
I have done several projects using PDF's from Autocad and they can be a real mess. I remember one that had over 12000 line segments in a single curve. The only solution was to go into Illustrator and start deleting the unnecessary extra stuff and unlocking and removing sometimes hundreds of useless empty paths and clipping masks.
Some files were helped a great deal by simply opening in Acrobat Pro and doing a save as PDF - Optimized and letting Acrobat clean up everything it could, then opening up the new saved file in Illustrator and splitting up the elements you need to be on separate layers.