Crewe boss Dario Gradi felt his side took control of the game after that but Megson said: "We had to make the changes because we have got people with one or two knocks.
"Friio picked up a calf injury, Commons (injured) his thigh. We wouldn't have done it if we hadn't got the injuries.
"The fact is that we were 1-0 up at half-time and looking quite comfortable. That is obviously a blow."