Once you log in to bricklink, there is also a "Upload" option under the Want menu that will allow you to upload an .LXF file. It will give you error messages on the offending parts. If you export a BOM from LDD, you can match up the error messages with the parts in the BOM to know where the issues are.
I have had issues with official parts not being recognized (brickheadz 1x2x1 2/3 SNOT bricks for example) so you may have to look up the parts on bricklink manually to confirm.