The g and b strings are tuned to a major 3rd rather than perfect 4th. While equal temperament 4ths and 5ths are close to their just intonation counterparts, 3rds are quite a bit off. Maybe thats what you are hearing.
This tends to be more a singers problem. Or perhaps a violin player. (fretless instruments played solo)
But guitars being setup to be just intonation kind of force us to become very used to it.
We just "know" when it sounds off, as the tuner in this case indicated, because we are forced into this intonation.
Ditto with piano.
I've tried putting piano to a singer after the fact (who sang solo) and ran into this difference. Singers are focused on their key while us guitar/piano players are looking forward to all the other possible keys to be played. It's why we're a little 'off'