Saints midfielder Schneiderlin was lucky not to be booked in the first half for a poor tackle on Mohamed Diame.
Referee Andre Marriner chose not to even award a free-kick for the two-footed challenge and was in the spotlight again in the second half after adjudging a Joey O'Brien lunge on Adam Lallana only worthy of a booking.
Hammers boss Allardyce felt the tackle was a red-card offence and told Sky Sports 1: "We feel a bit disappointed about the fact that Schneiderlin is still on the pitch. We didn't even get a free-kick and it was a two-footed challenge.
"We're told by everybody in the referee's department that a two-footed challenge is no other choice but a straight red - this wasn't even a free-kick.
"Andre Marriner is such an experienced referee and for the life of me I can't see how he didn't see that.
"For me, that was a disappointment as it kept them with 11 men on the field, when realistically, the way the law is portrayed today, they should have only had 10 men on. That would have given us a better chance of winning - but it didn't.
"I'm happy with the point, I can't affect what the referees do, it's not my job - but I have to point that I think that was a really poor decision...that's my responsibility.
"At the end of the day we're happy with a 0-0 draw, especially with our injuries. No Joe Cole, no Andy Carroll, no Stewart Downing today, no Alou Diarra - so I think it's a really good performance by the squad who have stepped in and done the job."
Jussi Jaaskelainen produced three stunning saves to keep the hosts at bay, but Irons defender James Collins wasted arguably the best chance of the games with six minutes left, steering a right-footed shot high over the bar from 12 yards out after Mark Noble had pulled the ball back to him.
"We could have won it at the end when Ginge had the chance he had for us, probably our best chance of the game," added Allardyce.
"Unfortunately it has fallen to the centre-half but at the end of the day from that far out he should at least hit the target and he's really disappointed.
"But overall it was a decent performance and defensively we showed how good we are. We've only conceded one goal in four games now but we just can't find the back of the net. Three games without a goal is my concern - and it's not as if we didn't create any good chances in the final third today.
"It's just eluding us at the moment, and when a golden chance falls like that at the end of a game, you want to put it in and walk away with three points.
"It was a good game, even though it was a nil-nil. Both teams went out and played and changed the style of play whenever you needed to. We sat deep, whenever we needed to shut them down from the front we did do.
"Our tactics were to allow them to play out from the back, shut them down and pinch the ball back - we did that brilliantly. Then that forced them into the longer ball off Lambert...that was difficult, but we did that well too.
"Sadly we couldn't find the quality to test the keeper more even though we got into some good positions - but it's a very well-earned point for us."
On Jaaskelainen's man-of-the-match display, Allardyce said: "He hasn't had a lot to do so far this season - but when we needed him today he was there three times particularly, and that's very encouraging as it gives the back four so much confidence."