Maher chose to freshen up his side following a gruelling schedule which has seen the Shrimpers play 15 games in 49 days.
READ MORE: All the details from Blues' defeat to Hartlepool
But the Blues chief confirmed some of the changes were down to injuries.
“Collin was injured and James Golding we’re having to manage because of an Achilles problem he has,” said Maher.
"The midfield, we wanted to give Leon (Parillon) minutes because he's coming back into it and we need him firing.
"We wanted to get Cav (Miley) minutes and Boyesy (Harry Boyes) and Keenan (Appiah-Forson) came back in but they've played most of the games anyway so there's not much change there."
The new look Shrimpers started brightly with Andrew Dallas putting them in front inside the first minute of the match.
But Maher felt Blues’ failure to score a second goal when on top proved key.
"We scored early and we were so much in control of the game in the first 15 or 20 minutes,” said Maher.
"We needed the second goal then because we were completely on top.
"We got into the final third a lot but we were missing the target with shots.
"We needed that second and then we let them back into it with a lapse in concentration I think because it had become, without being disrespectful, too comfortable at times.
"We make a mistake, we give a foul away, don't mark on the set piece and then it's level.”
And Hartlepool followed up their equaliser by scoring three goals in the second half.
"It's game on after their equaliser and we conceded a poor goal at the start of the second half,” said Maher.
"The third and fourth are really disappointing and from our point of view they're poor goals.
"I'll look at the stats later but I think we would've had 20, 25 shots.
"We've scored three but I’m disappointed we haven’t got more.”