Hammill was visibly disappointed with being replaced during the second half of the 2-0 defeat at Oakwell and appeared to shrug away his manager's attempts to calm him down as he left the pitch.
The 39-year-old told the Yorkshire Post: "It's not about him, it's a team game.
"Showing a lack of respect to his teammates is not on. He is frustrated, but I had a big problem with him not showing the lads respect."
Hammill has featured in each of Barnsley's 13 Championship fixtures this season.