Marcel Sabitzer and Niklas Süle were introduced as 86th minute substitutes but initially only one player appeared to make way, leaving Bayern with 12 on the pitch for around 20 seconds.
Referee Christian Dingert was alerted to the confusion by Freiburg players and stopped the match for a few minutes as matters were cleared up.
"I noticed that Niki came on and no one went off," Freiburg defender Nico Schlotterbeck told Sky television.
Bayern led 3-1 at the time before Sabitzer added their fourth goal in injury-time.
"I have to watch it again in peace," Freiburg sport chief Jochen Saier said. At the edge of the pitch there were intense discussions between Bayern officials and the referee.
Potential consequences are not immediately clear with Saier saying he "could not judge" what would happen.
According to the rules of the German federation (DFB), however, it is unlikely to impact the result.
Referee acted Dingert correctly in interrupting the game and as there were no goals scored by Bayern during their brief advantage, there seems little reason for altering the result.
