But life is sweet for Iron caretaker manager Russ Wilcox, who has boosted his hopes of landing the job permanently after a third successive win since he took charge.
Leading marksman Sam Winnall fired Scunthorpe ahead after just six minutes with his ninth goal of the season.
An own goal from Torquay centre-back Anthony O'Connor made it 2-0 on the half-hour before teenage substitute Hakeeb Adelakun wrapped up the points in the 61st minute with his first ever league goal.
A 78th-minute reply from John Marquis was too little, too late for the struggling visitors.
"We went in 2-0 down at half-time, but on the balance of play you wonder how that was," said a disappointed Knill.
"We told the players at half-time that if we could get the next goal, then it would be 'game on' for us. Unfortunately it was Scunthorpe who got the third goal.
"At the moment, a combination of bad luck and bad decision making is costing us dearly, but we have been saying that all season. The belief is there that we can turn things round, but we have to start putting some points on the board.
"I am under pressure as the manager and I know the club is under pressure too. But I will continue working hard to do my job until someone tells me differently."
There was sympathy for Knill's plight from Scunthorpe custodian Wilcox, who said: "I have a lot of respect for Alan. What happened while he was in charge here happened, but he has come back here and fronted-up and conducted himself well.
"If it is any consolation to him, I do not think Torquay look a relegation side. They came here and gave it a real good go and made it difficult for us."
- Sports & Recreation
- Russ Wilcox