Jones has been charged with bringing the game into disrepute for his scathing comments about referee Mark Clattenburg in the 1-0 win over Leeds.
Walton, who was controversially sent off for two yellow cards in the game, faces a charge of improper conduct.
As he walked from the pitch he kicked the electronic substitutes' board.
The referee's assessor's report confirmed that the on-loan Charlton man's dismissal for alleged diving was wrong, but that has not saved him from a charge.
Jones and Walton have 10 days to appeal, but will not know their possible punishment until after that period.
Cardiff striker Michael Chopra was also scathing in his comments on Clattenburg's performance, but appears to have escaped punishment.