The occurrence happened when the fourth authority showed some unacceptable number on the board and Kingsley Coman remained on.
The Bundesliga pioneers could see their success toppled after Freiburg's allure.
"I would have told my club not to continue with an allure," said Bayern's German mentor Nagelsmann, 34.
"I for one don't have the foggiest idea why Freiburg are doing this. I could never have done this is on the grounds that you are utilizing a slip-up of your adversary to get focuses due to the incredible strain from fans or backers," he added.
A court choice is normal this week, yet under German football administers any group which fields 12 players is rebuffed with the deficiency of the game and any places.
Alphonso Davies set for Bayern Munich return
Defending champs Bayern are looking for a tenth title in succession and hold a noteworthy lead over nearest challengers Borussia Dortmund.
Freiburg, in the mean time, are fifth - which addresses a spot in next season's Europa League. They are three focuses behind RB Leipzig, who possess the fourth and last Champions League position.
Should the outcome be toppled, the three focuses could demonstrate essential to Freiburg with six association games remaining and any discipline for Bayern could likewise offer Dortmund trust in the title race.
"It isn't so much that that they would have scored two objectives in those seconds," Nagelsmann said.
"I couldn't say whether you [Freiburg] can congratulate yourself assuming that you fit the bill for Europe due to the three focuses which you didn't win on the pitch.
"A method currently lies with the games court and in my view it can head one path. However, i'm no adjudicator."
Bayern's staff gave the player number that was wrongly shown by the fourth authority in the 86th moment, when Corentin Tolisso and Coman should be supplanted by Marcel Sabitzer and Niklas Sule.
Freiburg stopped an allure on Monday, saying they ended up in a predicament through no shortcoming of their own.
The club said the DFB's (German Football Association) lawful and procedural guidelines had "constrained" them to play "a functioning job in having the occasions legitimately explored".
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