The pair were among five players that came into the team to play Livingston and both started up front and struck their first goals of the season in a 2-1 win.
McHugh headed home from close range on 15 minutes and McFadden scored a wonderful second in the 70th minute when he flicked home Lionel Ainsworth's driven cross with the back of his heel.
McCall said: "I have to say, I thought Livingston were terrific and it was only really when they went down to 10 men that we had chances to kill it off.
"I think we did enough to win the game. I'm disappointed to lose the goal but overall we're in the next round and that's the main thing.
"The park was really wet and it was skidding off and things weren't coming off in the final third for both teams, but I'm pleased James got on the scoresheet and got a full 90 minutes.
"He is desperate to do well, he puts everything into training and games.
"Both strikers scored so that was great."
Livi had their fair share of possession but could not test Gunnar Nielsen and their comeback hopes were dashed when Jason Talbot was sent off for a reckless tackle on Stevie Hammell deep in Motherwell's half five minutes before McFadden's goal.
They kept going though and Danny Denholm bundled home a 90th-minute corner.
When asked about the red card, manager John McGlynn said: "I would need to see it again but I don't think you need to go in as aggressively in that position on the pitch. Away up there, what danger is anyone doing to you?
"It cost us because we were well in the game."
McGlynn added: "I thought we played some really good football and controlled large chunks of the game. Credit to the lads, we even got a goal back at the end."