However, Bedford roared back and with the home pack in strong form ran out 43-27 winners to claim a cup final spot against Bristol Rugby.
And Head of Skill Development and Academy Manager Stanley admitted turnover ball in key areas and the first half loss of Carlisle - who limped off with a hip injury - had proved pivotal.
"We're very disappointed to have come this far and put ourselves into this position and then not take advantage of it," said Stanley.
"Full credit to Bedford, they put in a good performance. But you always look at what you can control and we probably gave them too many opportunities to play the kind of rugby they wanted to, mainly by turning the ball over.
"There were aspects of the game that happened at various stages that went against us. Losing Joe Carlisle, when he looked to be in such good form, was a blow to us.
"The Blues took their opportunities when they arose and we gave them opportunities within the game with turnover ball. We said we weren't going to do that and in that situation we came off second best."
Warriors, who made 15 changes to the side that faced Bristol last weekend, burst out of the traps to stun Bedford in hot and humid conditions.
But a strong response from the Blues pack, who contributed four first half tries and two while Oliver Tomaszczyk was sin-binned, saw them run out deserved winners.
"It was a great start for us - better than we could have hoped for," admitted Stanley. "But again we didn't deal with the kick-off and allowed them to get good field position and capitalise.
"They pressed us down with the slope in the first half and, when someone goes into the bin we are down to 14 men, they took advantage with the scrum and the driving lineout. Small margins in the game can come back to haunt you and they did today.
"As the game went on we imposed ourselves a little bit in the pack, but when you get momentum in the game it can feel like the referee can go with that team in the 50/50 decisions.
"Bedford had momentum around the scrum area for the first 25 minutes, but we came back into it as the game wore on and were able to use it as a weapon."