Accies ran out 4-1 winners against Alloa, with Tony Andreu, Martin Canning, Louis Longridge and Eamonn Brophy scoring, although it was level at the break after Greig Spence's strike.
"I could have played a full-strength side but I thought it was an important game to give some of the fringe players a bit of game time and an opportunity to step up to the mark," said Neil.
"I thought we started well and moved the ball pretty quickly, we created a few chances but when we scored the goal we took our foot off the pedal.
"I think as soon as you drop your standards against any opposition you're going to find it tough, and to be fair to Alloa they scored a really good goal.
"I had a stern word with them at half-time and got a wee bit of a reaction. We brought some of the more experienced players on and I thought the difference was night and day. You could see the tempo of our game rise and we got a few goals which was nice."
Despite the result, Alloa manager Barry Smith was pleased with his side's efforts.
"I thought the boys, especially in the first half, created a few chances," said Smith.
"We can't take anything away from Hamilton, they had a lot of possession, but that's the way we set up to play. Was there three goals in the game? I'm not sure."