Clark predicted the midlands club could be on the brink of fresh success but he was not happy with certain aspects of Birmingham's play against the League Two club.
'They are a great bunch of lads. We have a great spirit. They want to learn and if they continue to do that I think we could do a lot more," said Clark.
"But to give away two goals indicated that something was not right. Fortunately we had enough in the locker to win. To give Plymouth the opportunities was the disappointing thing. It was a little frustrating and something the players will have to work on very quickly.
"We scored some great goals but I told the players at half-time that the name of the game is scoring goals and that there could be a shock result.
"They gave us a problem as they took us to extra-time but it was a fantastic winning goal from Kyle Bartley.
"The problem for me is that I sometimes forget how young some of the players are because they are inexperienced at this level. But they have to adapt quickly and change their mentality."
Bartley came from nowhere to slam home Birmingham's extra-time winner. The on-loan Swansea defender produced a perfect finish when he hooked home a right-wing corner from Scotland international Chris Burke two minutes into injury time.
Two goals from Scott Allan had earlier appeared to have put Blues through only for Lewis Alessandra to hit back with a brace to keep battling Plymouth in the game.