Macintosh HD>Library did not migrate. What else is missing?

I recently migrated to a new (identical) MBP Retina with the same OS 10.9.3 and chose to migrate everything. When I compared the two computers, I noticed the new one had about 30 GIG less than the old one. I went through with a fine toothed comb and noticed that the additional content I had downloaded for Logic Pro X which is located in Macintosh HD>Library>Audio had not transferred. Then I noticed that a lot of other data within the Library had not been transferred either. How did this happen and what else might be missing? How can I be sure I have everything I need? I thought ticking all the boxes in the migration meant that everything would be transferred.