The former Borussia Dortmund manger was clearly frustrated with the Swiss international after late goals from Emerson Palmieri and Eden Hazard condemned Liverpool to their first defeat in any competition this season.
Klopp was seen gesturing at Shaqiri to press higher multiple times throughout the Wednesday night's league cup fixture but told reporters this was not the cause for the heated exchange after the game.
It turned out Klopp thought Shaqiri should have been more assertive and delivered a late free kick to Egyptian ace Mo Salah, rather than let Jordan Henderson waste the opportunity with a delivery into the box.
Speaking in his post match press conference the German said:
''I spoke about a free-kick, the last one,' said Klopp. 'We wanted to have Mo a bit wider, so we had passed the ball to Mo, the whole bunch of players was in one direction - where we shot the ball, actually.
''But if we can send Mo into a one-on-one situation in the last situation of the game, it would have been not too bad. What I said was about the free-kick, nothing else.''
As well as the dead ball situation, Klopp did not look happy when the former Bayern Munich and Inter attacker stayed down to appeal for a penalty rather than play on earlier in the game.
Shaqiri has seemed difficult to manage in the past and Liverpool fans will be hoping that the case is not the same at Anfield.