Heynckes, well known for his ability to keep his men in order, has enjoyed a good start to the season since taking over at Bayern following the sacking of Louis van Gaal last term.
Despite the Bavarian outfit missing one of their star players in Robben through injury, Bayern have not skipped a beat in their bid to reclaim the Bundesliga title which they lost to Borussia Dortmund last season, and only on Saturday hammered Freiburg 7-0.
In-form Mario Gomez hit four in that match, while Franck Ribery showed signs of returning to his best with a brace.
But while many believe Robben's impending return will only strengthen Bayern, Schuster feels the Dutch international could give Heynckes a headache with his selfishness.
"I do think that Robben is a problem for Bayern this year," Schuster told Sport1. "I think the philosophy of the team is different under Jupp Heynckes.
"Robben is incredibly stubborn. He does what he wants to do, regardless of Gomez and Ribery's positions.
"Of course he has class, but this is a problem.
"Their game is fluid at the moment [and] he may slow it down."
Schuster is currently unemployed having left Turkish giants Besiktas in March, and has been linked with taking over at Hamburg, whose current coach Michael Oenning is under signficant pressure after a woeful start to the season.
And the ex-Real coach admits managing a side of Hamburg's stature is always going to appeal to him.
"If a coach has no job, HSV are always interesting.
"At some point, I'd like to be back in the fold in Germany.
"I had two or three opportunities to come to Germany. Two years ago, I spoke with Bernd Hoffman [former Hamburg president] about the HSV job."
Schuster's only previous spell in the Bundesliga was during the 1998/99 season with Cologne, before he ventured overseas and managed at clubs like Xerez, Shakhtar Donetsk, Levante and Getafe.