Do you have any duplication in your address book? Is your friends email address and phone number stored in the same contact? I imagine this would be worth checking. If this doesn't help, delete the sms and imessage conversation streams and start a new one by sending him a message... it should just work.
This is happening with my wifes conversation with me, i get seperated messages from her, mine are collated properly on hers. I have found the issue is that on hers her phone number is missing from
Settings >> Messages >> Recieve at
On mine in that position my phone number is there and is greyed out as is all my colleagues. My wifes however the phone number is missing and it doesn't allow you to add it, so is using her email address for iMessage.
So i message her and it sends as SMS but when she replies it comes as iMessage.
First see in https://appleid.apple.com if her apple ID is linked with her iPhone phone number, if not, modify and save changes, then in her iPhone go to settings -> messages -> and deactivate iMessage and activate it again (the phone number should appear in "Receive At" greyed out). Do the same in settings -> FaceTime. After that reboot your iPhone. Hope that works, it worked for me