Brazilian Breno also angered club bosses this week by venting his frustration on Twitter after being forced to play in the reserves at the weekend.
"This is all very unfortunate and should not happen," Heynckes told reporters on Thursday. "But this is not the moment to start beating the young man.
"He must not overstretch it but he is more in need of support and help than punishment," said Heynckes before adding Breno had gone through a difficult time in his life.
The 22-year-old spent several days in prison last year before posting bail in an arson case involving his own house.
Bayern told Breno on Tuesday to stop criticising the club after he wrote on Twitter: "I do not want to talk badly about the B team but I go to play a friendly.
"In this phase I am going through at Bayern they are messing with me."
Breno joined Bayern as an 18-year-old but has yet to hold down a regular starting spot.
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