Visiting keeper Michael Ingham made crucial saves to deny Karl Hawley and Billy Bodin and just a minute later Wes Fletcher scored on the spin for the Minstermen from Craig Clay's cross.
Josh Carson made it 2-0 from a 67th minute free kick despite keeper Martin Rice palming the ball onto the bar.
Rice could do little about former Gulls striker Ryan Jarvis making it 3-0 from close range in the 73rd minute after he saved David McGurk's initial header from a Carson corner.
Knill said: "Goals change games and we switched off three times and they scored and we lose 3-0 at home, so you are definitely open to criticism. You just have to accept it.
"I have got to say in the first half there was nothing in it really. If anything we were the better team but you need to score.
"Then we come out in the second half and nearly score at one end then concede at the other. Straight away you say 'okay it's 1-0, we don't want to concede, but we are still in with a chance here. There's nothing in the game'.
"Then he puts it in from the free kick and it becomes a struggle. It's down to fine lines. It's what we all talk about before the game isn't it? Fine lines.
"If you switch off, you give the opposition the opportunity to score, and we switched off at the throw-in, free kick and corner.
"When you work on stopping those specific things, you have to hold your hand up and take the flak. We will do that and then it's all about how you respond.
"When you are at home it's irrelevant how well you play, you have to win."