Bought a brand new 2017 Honda rebel?

Never owned a bike before just got this bike up to 80 miles today and noticed when I shift the click noise is starting to get more noticeable is the bike just getting broken in and thats normal or do I have problems

Maybe the clutch needs adjusting? Revisit the dealer to have it checked.

What "click" noise exactly?

An engine won't be run in, until it's covered several thousand miles.

There's a tightening bolt on the shifting lever where it meets the shaft (usually a 8mm head), make sure it hasn't loosened as the free-play makes things a bit more noisy.