It was a gutting late blow for the Shots, who took the lead in the second half through Jake Gallagher.
But Josh Hare's leveller deep into injury time denied Gary Waddock's side of remaining the only team to have won all of their games.
"Obviously conceding a goal so late in the game is always disappointing but let's not forget that it's a point away from home," he told the club's website.
"We had chances and I thought their goalkeeper played extremely well and also Jake Cole has pulled off some great saves as well.
"There's going to be a lot of twists and turns in this league campaign and unfortunately we've conceded a late goal.
"You have to give Maidstone credit. They kept going, they made it difficult and were strong and physical. We had to stand up to that challenge, I thought we did apart from the goal."