A minute's silence in memory of the tragedy at Sheffield Wednesday's ground for an FA Cup semi-final 23 years ago was staged before both last-four encounters, but the occasion was audibly marred the second time around by a number of fans booing and chanting offensively.
Chelsea released an official club statement on their website after the game condemning the disturbance, saying: "Chelsea Football Club is extremely disappointed that a very small minority of fans embarrassed the club today by not honouring the moment's silence before kick-off.
"Chelsea FC believes all moments of respect should be honoured and today we pay our full respects to all those that suffered as a result of the Hillsborough disaster 23 years ago.
"The club will be working with Wembley and the FA to identify those responsible and if we are provided with evidence that season-ticket holders or members have been involved we will take the strongest possible action against them."
Chelsea went on to defeat Tottenham 5-1 and will return to Wembley in three weeks for the final against Liverpool.