Freiburg have launched an appeal against Bayern Munich after the Bavarians temporarily played with 12 men during their Bundesliga encounter on Saturday.
Bayern Munich won the game 4-1 to enhance their push for a tenth straight Bundesliga title while Freiburg's Champions League ambitions took a hit with the defeat.
The controversial moment occured in the 85th as Bayern led 3-1 when they messed up a substitution.
Bayern prepared a double substitution but Kingsley Coman remained on the field as his old number 29 was held up instead of the current 11.
The mix-up saw Marcel Sabitzer enter the field of play with Coman still on the pitch and the game continued for 17 seconds before the error was realised, leading to a lengthy delay to sort things out.
Freiburg could be awarded a 2-0 win if they are successful with their appeal.
"In the end I'm not surprised, to be honest," Nagelsmann said. "It is a procedure that lies with the DFB sports court. It has to make a judgement. In my opinion it can only go one way.
"From a personal point of view I don't understand it. Freiburg would not have scored two goals in those 18 seconds.
"I personally wouldn't have done it. I find that you are exploiting the mistakes of a third party to maybe score points yourself.
"I don't know if you can pat yourself on the back with the sponsors at the AGM in November if you play internationally because of the three points you won, which you actually didn't win in sporting terms.
"I wouldn't be so happy if that were the case. I would have clearly communicated to the club that we would not appeal. In the end everyone has to decide for themselves."