"It's something that shouldn't really be happening," said Jordan, who played for United between 1978 and 1981.
The chants heard at Old Trafford included: "It's never your fault, it's never your fault, always the victims, it's never your fault."
But the Manchester United Supporters' Trust (MUST) insisted they were not a reference to the Hillsborough tragedy.
"Following this week's developments and release of revelatory information on the Hillsborough tragedy, MUST wishes to make it absolutely clear that, just as we condemn chants mocking the Munich air disaster, we also condemn any chants relating to Hillsborough, or indeed any other human tragedy," said MUST chief executive Duncan Drasdo.
"We did hear the usual anti- Liverpool chants at the match today but we're pleased to say, despite some reports to the contrary, there was nothing that was specifically referencing Hillsborough."
The findings of an independent report, released last week, cleared Liverpool supporters of blame for the deaths.