Alex Revell stepped up to equalise at 1-1 for the Cobblers before United eventually overcame the League One club 3-1.
Mourinho also felt Northampton should have had Jak McCourt sent off for a challenge on Memphis Depay shortly after half-time.
Regarding the penalty, Mourinho told Sky Sports and MUTV: "Well, I think I should stop speaking about the referee's decisions and I should just wait for you to speak about it.
"Some with an honest vision, some with a dishonest vision, but I should just wait a couple of minutes.
"The game should have been easier. We should have been playing against 10 men very early in the second half.
"The red card was a dangerous situation, and I am not speaking about the penalty. I am speaking a situation that could happen and what could have been an important injury.
"Even in this kind of situation I should stop and leave it with you."