It sounds like he's not yet comfortable with many alternative sounds. He's obviously using phonics very rigidly, which is standard at blue level but really not at purple level.
The examples you've given are all completely phonetically decodeable and should be taught as such.
Phone - split digraph o_e making it's most common sound.
Shone - split digraph o_e making a far less common sound: shone, gone
My - this is the most predictable spelling. In a single syllable word, y says "igh" - fly, try, by, shy. It only says "ee" as a second syllable - happy, shiny.
Your child seems to be at the stage of wanting to stick rigidly to the phonic rules he's learning. Which is fine. Using mixed methods (ie. Not following phonics only) at this stage may actually delay his reading progress longer term.
What does seem odd is the discrepancy between his band from school and his abilities. I would suggest you ask the teacher what he's currently learning in phonics and request a reassessment to see if he's ready to be moved forwards - his book band will (or certainly should) be linked to his phonics learning, or phonics group if children are grouped.