Looks like dealer assembly damage. I got to see my bike in the crate after it came off the truck. Kawi sends them with the bars off, and a metal tab from the top of the crate frame bolts to the tree to hold the bike upright.
So the dealer has to remove those bolts from the crate tab, and them use them to bolt the bars in place. Looks like the dealer's shop might have been a bit rough with them, and damaged the black oxide coating. Or they got beat up when the factory was putting in the crate. No way of telling really.
Pull the bolts and wire brush them off, then spray with some rustoleum, or go stainless, would be the best way. There might be some plastic hex bolt caps at the hardware store, but wouldn't bet on it.
On my Seca, it has plastic caps over the hex bolts on the bars, so they do exist. If you have a sharp parts guy, he might be able to looks some up for you.