The Bayern Munich sporting director is frustrated at the lack of refereeing consistency that saw Bastian Schweinsteiger shown a red card but not the opposing winger
Already on a booking, the Ecuadorian threw himself into a challenge with Jerome Boateng during the two teams' 1-1 draw on Tuesday night.
He escaped punishment from referee Carlos Velasco, although the official later sent off Bayern goalscorer Bastian Schweinsteiger after the midfielder picked up a second caution for a foul on Wayne Rooney.
"If you apply the same standards then I don't know how Valencia stays on," Sammer told Sky. "If the referee has a policy, then he must go through with it.
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Many had thought that holders Bayern would brush aside a faltering United on Tuesday but David Moyes's men held their own to remain in with a chance heading to Munich.
Despite the two sides' differing fortunes so far this season - Bayern have already retained their Bundesliga title, while United sit seventh in the Premier League - Sammer insists that he knew that the tie would be no straightforward task.
"We sounded a warning ahead of the game in Manchester but people turn a deaf ear at times," he stated. "They played just as we expected. They were very strong physically, organised and they tried to play on the counter.
"They managed that really well and they made life difficult for us but that's what you expect in the Champions League - it's the top level of the game so we accept it and we're happy with the result."