Despite winning the Tuesday night tie on penalties it was a below-par display from the Stark’s Park side in a drab 0-0 draw which saw the hosts create the better chances during the 90 minutes.
Raith huffed and puffed throughout but failed to find the rhythm to their play which has so often been on display this season and has taken them to the top of the Championship table.
Speaking to Raith TV, manager McGlynn called the performance “poor” and admitted it had taken him by surprise.
“It's not what we've been used to but we're through,” he said, “I think that's as much as you can take from it.
“It was well below the standard we are capable of and what we have been producing.
“In the law of averages with all the good performances we've put in, maybe we were due one.
“There's no real excuse for it. Everyone who was on the park has been doing well.
“We made a few changes but it shouldn't have had as much of an impact as it did on the game.
“From our point of view it was a poor performance from us.
“Robbie Thomson pulled off one tremendous save in the second half. The boy was through one on one with just Robbie to beat and he made a great save.
“We didn't create an awful lot, maybe two or three chances max. One in the first half, maybe two in the second.
“Smudger (assistant manager Paul Smith) and I are scratching our heads a little bit. We couldn't have complained if Inverness had won in the 90 minutes.
“I'd like to thank the travelling support who came up.
"I know they'll be happy because we won, but they travelled a long way and we should be putting on a better performance than that.
"We gave some valuable minutes to the guys who got on. I think both teams did that.
"Inverness put on some young players as well and they had made some changes to what would be their normal starting line-up.
“It keeps the run going and takes us on to Arbroath at the weekend but we'll need to play better than we did tonight, that's for sure.”
One plus point on the night was the performance of goalkeeper Robbie Thomson who replaced the regular Rovers no.1 Jamie MacDonald and put a good display, saving two penalties in the shootout as well as one outstanding stop in the second half from Caley striker Lewis Jamieson.
“It was a great save,” McGlynn said.
"He works hard with Jamie MacDonald and got a chance tonight.
Jamie's wife is due to give birth any time soon - the sooner the better hopefully! - so Robbie went in goal tonight, made a great save and pulled off a couple of great saves in the penalty shootout too.”
Despite being unhappy with the display McGlynn said he was happy to have got to the semi-final of the competition in which Raith are the trophy holders after sharing it with Inverness after last year’s final was called off die to the coronavirus pandemic.
He said: “We're delighted to get through.
"It gives us another game and obviously with getting through in the Scottish Cup last weekend we now have two cup ties to look forward to in the new year.
“The support is going from here to there. Down to Kilmarnock then up to Aberdeen for Banks O' Dee as well.
“Getting to the semi-final stage might whet the appetite for a few of them to go down to Kilmarnock and I don't think we've played Bank O' Dee before so that'll be a new experience for them.”
He addded: “We're doing well in the league too so there's a lot to look forward to.”