Go to the phone menu and then ask Sync to "read message". On my car sometimes the message notification persists on the radio even though I've already read the message on my phone. Sync may read it or it may say no messages, hopefully this will clear it.
2013 GT Premium Brembo
MGW, Blow Fish, AM Hood Struts
Tinted, Borla Touring AB, ProCal Tune
Full Shelby/Kicker Audio Upgrade