The Rangers left-back has been named in previous squads by national team boss Gordon Strachan but failed to make the cut for the clash at Wembley.
Wallace may be plying his trade in the Scottish League One but McCoist expressed his surprise at the defender's omission for the first meeting with England in 14 years.
And the Light Blues boss is confident Wallace will again catch the eye of Strachan if he continues his fine early season form.
McCoist told RangersTV: "Lee has done really well so far this season and I'm a little bit disappointed he's not in the squad.
"I'm sure he'll be a little bit disappointed too.
"Gordon has picked his squad though and we have to respect that.
"I'd be very hopeful that if Lee keeps performing the way he is, it won't be long before he's back in there.
"That's what he has got to aim for.
"Lee's attitude, as everyone can see, is absolutely first class and it's how he reacts to the disappointment of being left out that's important."
Meanwhile, McCoist plans to arrange some practice matches to ensure his new signings are ready for action when they can finally play competitive matches for the club.
A transfer embargo means Rangers must wait until September 1 before registering the eight players who have so far committed to joining the Glasgow side.
Nicky Law and Jon Daly have both featured as trialists and McCoist is keen to make sure the rest of his new recruits are just as sharp when called upon next month.
McCoist said: "We've had a couple of [friendly] games recently against Dundee and Newcastle United which have been very beneficial.
"We have been speaking about it and we'll probably get a couple of closed-door games arranged at Murray Park.
"We just want to keep everyone ticking along nicely so that they're ready to hit the ground running come the start of September.
"With the pre-season they've done, they will be."