The Blues issued a statement condemning the behaviour of "a very small minority of fans" before their 5-1 win over Tottenham.
A statement on the club's official website read: "Chelsea Football Club is extremely disappointed that a very small minority of fans embarrassed the club by not honouring the moment's silence before kick-off.
"Chelsea FC believes all moments of respect should be honoured and today [Sunday] we pay our full respects to all those that suffered as a result of the Hillsborough disaster 23 years ago."
A small number of Chelsea fans chanted during the silence, a mark of respect to the 96 Liverpool fans who died at Hillsborough during an FA Cup semi-final between the Reds and Nottingham Forest.
Other fans booed the disruptive group when the silence, also in memory of Livorno's Piermario Morosini, was over. Morosini died on Saturday after collapsing on the pitch during his side's game with Pescara.
Liverpool's last-four clash with Everton took place on Saturday to avoid be played on the anniversary of the disaster.