Re: is this common?
I would have a tech check it out--sometimes the key heights of the open tone holes (those below the notes you're playing) are set too high. This can affect intonation. Also, if the E and D keys aren't closing completely, that could also cause those notes to be sharp. A tech could check this out.
Some saxophones, particularly sopranos, are known to be out of tune, but I haven't heard that about Yani's. Some people on this forum love them--I know nothing specific about them.