Paul McCallum had given the Shots a third-minute lead but second-half goals from Robbie Weir and Michael Symes gave the Brewers all three points to leave Scott to focus on a vital clash with AFC Wimbledon on Saturday.
He said: "In the first 20 minutes we were well on top and very comfortable but we took our foot off the gas. We let them back in the game, because we were as comfortable as we have been since I've been here.
"Everyone started thinking we could do something different and not follow the script. We gave the ball away cheaply, free-kicks. They scored from the edge of the box when we didn't do our jobs again.
"When we showed some urgency towards the end we caused them problems, but it was a complete dip from the last four games. We didn't stick to what we have done well.
"You can get carried away a bit. We've come in because there are problems. We saw the frailties in areas we haven't seen. But we shouldn't be surprised, we can't mope. We have to understand why we lost.
"But we have to go again on Saturday because it's a big game."