Luca Toni and Philipp Lahm are both facing disciplinary problems at Bayern Munich following a 1-1 draw against Schalke on Saturday which saw the team slip to eighth in the Bundesliga.
Italy international Toni was replaced at half-time by coach Louis van Gaal and, according to reports, left the stadium immediately rather than taking his place on the bench in the second half.
Team-mate Lahm angered club bosses with an interview he gave to the Suddeutsche Zeitung newspaper before the game in which he criticised their transfer policy.
Hoeness says both can expect to feel his wrath in the next few days.
"I will not criticise him (Lahm) in public and I will only talk about his performance in my office, but what I can say is that it would have been better had he not given this interview," said Hoeness.
"He has broken club rules and he is going to regret it."
As for Toni, his future at the club is looking bleak after his apparent half-time disappearance.
"That was wrong and we have taken note of it," commented Hoeness.
Only Van Gaal escaped criticism even though his position is looking precarious on the back of yet another disappointing result.
Bayern, who are also on the brink of elimination from the UEFA Champions League, lie six points adrift of league leaders Bayer Leverkusen, their next opponents in a fortnight.
Between now and then, Van Gaal will be working harder than ever on finishing after seeing his team once again scupper chance after chance.
"We had the chances, but were always just two, three or five centimetres away," he said.
"That has got to change. It is frustrating that we didn't manage to score in the second half. We would have deserved that."