[jblackburn]

I think it needs either the head unit replaced, software updated, or if the bluetooth/USB module is still separate from the head unit like in the Gen 1, that may be your culprit.

The 2016 LT's (7" HU, same as yours) I spent a good few weeks in had no issues with Bluetooth and connecting to my iPhone 6; my 2016 Premier with the 8" HU occasionally doesn't connect to Bluetooth unless I go into settings and tell it to find the phone. Both would occasionally skip or stumble when CarPlay or Spotify opened until you unplug and re-plug in the phone, but I think that's more to do with my phone being an idiot, as it does the same thing in my friend's Civic.

 

[jblackburn]

Should the head unit be covered by warranty? Provided i take a week off work to get it handled.

Call ahead of time and ask if they'll give you a rental.

Should be covered by warranty. Sit there with the service advisor and demonstrate what it's doing so they can write it up as such.