The two clashed after the clash at Stamford Bridge last season and Bethell was charged with improper conduct and for using racist language.
“We are surprised and extremely disappointed that the decision to charge the club has been taken nearly five months after the incident,” Chelsea said in a statement on their website.
“The charges will be contested as we understand that no racist language was used and that Sam Bethell was doing no more than trying to defend himself. Chelsea FC is deeply committed to stamping out racist behaviour and would never condone it.”