Rovers fell to a Graham Carey strike and a dubious Jake Jervis penalty before Liam Mandeville missed a late penalty and James Coppinger was sent off.
"In any game you play, particularly one like this one with first against third, you need a few breaks to decide something which is going to be quite tight," Ferguson said.
"I didn't think we got them.
"Some of our stuff was good.
"The first goal in a match like this, particularly with the way that Plymouth set up, was always going to be key.
"A lapse of concentration has cost us.
"We were in complete control of the game for large parts of it.
"It's a bad result but we will react hopefully as we do when we have a defeat."
A mistake from Andy Butler led to a fine strike from Carey to give Plymouth the lead.
Butler conceded the penalty but could do little about it as Ryan Donaldson ran straight into him. Jervis converted confidently.
Ferguson was unhappy with referee Oliver Langford's decision to award the spot kick.
He said: "You hope you get one or two decisions.
"The lad has ran straight into Andy Butler and the ball is already in Marko Marosi's hands.
"He's run straight into him. The ball has run away from the lad.
"The referee has made a decision and we feel it was very soft.
"It's made it difficult for us but at that stage we still felt we could get something out of the game.
"We needed a bit more quality at times in the box."