The Warriors didn’t play particularly badly, but conceded two goals through Blair Malcolm and Robert Buchanan early on and were unable to recover, despite Jamie Longworth pulling one back.
And Ferguson says his side will need to be stronger when they face promotion play-off rivals Elgin at Ochilview on Saturday.
Stenhousemuir have had mixed fortunes in their three previous meetings with the Highlanders.
They were outplayed on both of their visits to Borough Briggs, going down 2-0 each time, but were comprehensive 4-1 winners at Ochilview in December.
Elgin go into the match just four points and one place behind Stenny who occupy the fourth and final play-off spot.
Boss Ferguson said: “Elgin have a lot to play for and will probably see it as a game they have to go and win.
“They’re going to be fighting and scrapping for everything and we have to match that part to begin with.
“We need to make sure that we do not allow Elgin anything cheaply but still continue to try and play on the front foot and get forward as much as we can.”
On the Cowdenbeath defeat Ferguson said: “You could say we left ourselves a bit much to do. It was strange because I think in terms of our general endeavour, I can’t criticise the players at all. That part of it was there.
“What I will criticise the players for is their mentality, because their goals came too easily. We’ve shown over the course of the season we generally compete very well, and the win against Peterhead was a very good example of that, but I didn’t see enough of it.
“Our work rate was excellent, but our mentality let us down. We need to improve that.
“Between now and the end of the season we’re going to be coming up against teams fighting for something.
“Every game between now and the end of the season is a cup final.
“I think all we are missing is a ruthless streak, but our work rate and our general play was good, so if we can add that final element to our game, we’ll be fine.”
Stenny started well against Cowdenbeath, with Colin McMenamin heading the first chance of the game well over the bar from Mark McGuigan’s cross seconds after kick off.
Bradley Smith did well to test the palms of Lewis McMinn from 20 yards on seven minutes when he drove through the middle of the home side.
Then McMenamin found himself with another headed chance minutes later from a Nicky Paterson corner, but could only nod the ball into a relieved David McGurn’s arms.
Cowden’s Jordyn Sheeryn came very close to opening the scoring when he rattled the junction of McMinn’s post and cross bar from the edge of the box after a terrific run.
But moments later the visitors did have a surprising lead when Malcolm followed in Buchanan’s effort which rebounded off the post to fire high into the net from close range.
If the bottom side taking the lead was surprising, then Cowdenbeath’s second goal just before the half hour was near shellshocking for the home side.
Buchanan, who had been unlucky not to score the opener, was given far too much space by the Stenhousemuir defence, and jinked in from the right hand side before firing expertly past McMinn.
Moments after the half-time break, McMenamin found himself with a golden chance to put Stenny back into the game when Alan Cook played an inch perfect ball across goal to the front man, but the big number nine was once again foiled by McGurn.
Stenny spent most of the second half on the front foot, but Cowden stayed resolute until Ruaridh Donaldson crossed for substitute Longworth to head the home side back into the game from close range with 15 minutes to go.
Harry Paton struck the post soon after, then Longworth fired wide from the edge of the box as Stenhousemuir pushed hard for an equaliser in the closing stages but Stenny’s endeavour came too little too late.