Reflecting upon the game, McCall was quick to give opponents Southend credit for their hard-working display, stating that they prevented City from finding top form for most of the match.
City did have one purple patch in the game towards the latter stages of the first half when Marc McNulty opened the scoring with his first goal for the club.
McCall's men couldn't find a second goal before the break, however, and Southend went on to equalise in the second period through midfielder Anthony Wordsworth.
Speaking after the match, McCall said: "We are naturally disappointed not to win the game because we always set out to win our home matches, but I think we didn't deserve any more than a point.
"We are disappointed because we've took the lead and not gone on and won, but all credit must go to Southend.
"They are a big, strong, physical side and they played to their strengths tonight (Tuesday).
"We had a little spell in the match - probably 15-20 minutes just before half time - where we got our goal and we had two or three other good chances.
"If we'd scored again then, we could have gone on to win the game.
"On the whole though, they have defended well throughout the match and we've perhaps just lacked that killer pass at the right moment.
"It was stop-start at times, it was scrappy at times, and we just didn't quite manage to get into our flow in terms of our passing, apart from that spell before the break."
Goalscorer McNulty was one of four changes made by McCall to his starting XI, with Rory McArdle also handed his first league action of the season.
McCall added: "He (Marc McNulty) is different to what we've got.
"He likes to play on the shoulder and get in behind. He's also a top class finisher which he showed tonight.
"We knew Nile Ranger would be a handful for them but I felt Rory came in and did a good job against him.
"Him and Nat (Knight-Percival) did well against a lot of long balls into our box.
"When we play Saturday-Tuesday-Saturday, we will look to make changes, as we did when we played Fleetwood Town here on a Tuesday a few weeks ago."
After missing the last six games through injury, James Hanson made a welcome return from the bench as a second half substitute.
McCall said: "James has missed a lot of football and he is frustrated himself clearly.
"He has been working really hard and he is desperate to get back out there on a regular basis now."