Q: transfering files with migration assist

Welcome to the Apple Support Communities

That's the problem of using Migration Assistant. If you transfer your data during the first OS X startup, this doesn't happen.

Now, if you want to merge the files of both users into the first one, you have to log in the new user that Migration Assistant has created, and then, you have to put all the transferred files into /Users/Shared, or putting them into an external drive. Finally, log in your first user and go to /Users/Shared or the external drive to copy them to your user. It's long, but this works

Transferring files from one User Account to another