Kane endured a quiet afternoon at Wembley as United came from behind to book a place in the FA Cup final and inflict an eighth straight semi-final defeat on Spurs in the process.
Kane, who has scored 37 goals in 44 appearances across all competitions for Spurs this season, struggled to impose himself as Tottenham lost 2-1 to United at Wembley.
Both Spurs and United were left angry by the joke at Kane's expense and sources said the striker, who could captain England at this summer's World Cup, was bemused and disappointed by the tweet, which came at the end of a hard week for the player and his club.
The FA have apologised for a tweet which was posted on line during Manchester United's FA Cup semi final win over Spurs on Saturday.
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The account is run in-house by the FA and the tweet also left senior figures at the organisation furious.
In a statement, the FA said: 'We have written to both clubs to apologise for any offence caused'.
Smalling and Kane both play for England and could be in the squad for this summer's World Cup if manager Gareth Southgate calls on the pair.
When it was put to him that he did not seem quite at his best since the injury, Kane said: "I feel good, I feel sharp". It's been a tough week, a tough week for the team.
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