The Swans progressed to the fourth round with a 3-0 victory at the Liberty Stadium on Tuesday, in a match during which they had only nine shots to Everton's 11.
While Martinez conceded that his former club's clinical finishing meant that they were deserving winners, he insisted that the margin of the defeat was harsh on the Toffees.
"The game went down to whoever was going to take their chances," Martinez told reporters. "We started really well and stopped Swansea from being their normal selves, from controlling their normal football and we had two very good opportunities.
"If we had scored the first goal it would have been completely different. The scoreline reflects that Swansea were very clinical and we weren't and that is the reason why we are not in the competition.
"I feel Swansea deserve to go through as they had spells when they looked sharp and were good technically, but I don't think it was a performance which reflected a 3-0 difference."
Everton return to action when they visit Liverpool for the Merseyside derby in the Premier League this weekend.