Jonas Eriksson awarded the spot-kick in the 28th minute after Marc Albrighton clipped Antoine Griezmann as he attempted to cut into the penalty area.
The French forward stepped up to slot home the penalty and give his team the advantage heading into the return leg.
However, TV footage showed the initial contact was outside the box and goalkeeper Schmeichel did not hold back in his criticism of the decision.
"It's plain and obvious to see," the 30-year-old told BT Sport. "It's ruined our game plan, it's a decision that's very tough to take when it's so clear and so obvious and we should've had something from this [match] but we have to accept these things."
Read the full article on eurosport.co.uk: Schmeichel unhappy with referee over penalty decision