iMessages not showing some Contact names

After upgrading to OS X 10.11, El Capitan, I have noticed that several of my iMessage threads are showing the phone number only and not the contact names. I have checked my Contacts on my MacBook Pro (Early 2011) and the name and nickname is listed in the contact. Nothing has changed across my other devices. Is anyone else noticing this issue, if so have you been able to correct it?