Berbatov slotted a loose ball in the box past Joel Robles to cancel out Steven Naismith's opener before Bent grabbed the winner less than three minutes after coming off the bench in the second half.
Martinez said: "We had two or three great opportunities, but couldn't take advantage so that's a disappointment.
"We lacked a bit of composure in the final third and that cost us.
"There are many things we need to learn form it."
One crumb of comfort for Martinez was the performance of Barcelona loanee Deulofeu, who caused Fulham's defence problems all night with his skill and pace.
"He's a real threat," the Spaniard added.
"His play deserved more goals in the first half, and that would have been the difference."