Although Spurs managed four goals in a thrilling game that went to extra-time, they conceded five to see their cup run come to an end in the fifth round.
It is the first time that has happened to a Mourinho team since January 2015, when Chelsea were beaten by a Mauricio Pochettino-managed Tottenham.
Renowned as a master of defensive organisation, the Portuguese has struggled to bring that particular quality to north London.
But he might well wonder whether he has the right tools to construct a mean defence, or whether some serious work in the transfer market is required.
Toby Alderweireld was handed a new deal just a month after Mourinho arrived at Spurs, but it is possible that decision is already being regretted.
Alongside him, Davinson Sanchez provided two goals from set-pieces to help bump his FC rating up to a respectable 7.8, though he was far from defensively perfect.
The Colombian won eight of his 12 duels and made four clearances but couldn't help Spurs keep the hosts at bay.
Behind them, Hugo Lloris was perhaps a victim of some brilliant finishing, though he conceded as many goals as he made saves (5) and has faced questions over his reliability before.
It appears Mourinho has plenty of work still to do if Tottenham are to become a regular challenger under his guidance.