Veteran striker Jamie Cureton squandered his side's best chance of an equaliser on the hour with a poor finish after coming off the bench and Yates also felt the visitors had got a raw deal from referee Darren Bond.
"We thought we could have had two or three penalties, but the decisions have all gone against us," groaned Yates. "But to be fair, it was not because of that we lost the game.
"We lost because we committed the cardinal sin again of conceding a goal in the opening five minutes. It was a poor goal for us to give away, the first time they had got the ball into our box - and that gave Scunthorpe a lift.
"The effort was there from us in the second half, as I am sure the fans could see and we had numerous chances but just could not take them.
"It is definitely frustrating to get nothing from the game - but that early goal was the problem.
"All we can do now is keep believing in what we are trying to do and work even harder to achieve it.
"But just talking about it won't do any good, we have got to put it into practise. Everyone has got to raise their game. Things will turn for us, I have no doubt about that."
Winger Etienne Esajas fired the Iron into an early lead with a sweet left foot shot from the edge of the box for his second goal in successive home games.
But they then wasted a catalogue of chances before substitute Sam Winnall finally eased any nerves in the 90th minute.