With the other rafters having the 1”x6” band-aids covering them, my thought is the only one left exposed was their best of the job, so it was left exposed. There is a lot of variables with this type of framing that can cause gaps, shrinkage, cracks (checking), etc.
I start with what is this doing? In this case, it was mostly cosmetic. The tenon appeared solidly in the mortise.
Note it. Explain to the client that it doesn’t look like something that needs fixing and move on…after twenty minutes in that sunroom looking at all the timbers.
If the mortise and tendon were flush when the wooden pegs were installed either the wood pegs sheared off or the tendon split out a chunk the thickness of the pegs.