Steve Agnew says Boro were punished for starting poorly against Bournemouth on Saturday.
"We weren't happy with the start of the game, and that's where we lost it," he said.
"To concede two goals like we did was naïve and poor, and it gave us a mountain to climb.
"We changed shape going into the game, but the result today is not about the shape and systems. It's about defending and in those areas we need to be better.
Agnew says Boro's focus now switches quickly to Wednesday's Tees-Wear derby with Sunderland.
"The players have fighting spirit and will continue to fight," he said.
"We're all very disappointed but we have to dust ourselves down.
"We've got a huge challenge ahead but it's still alive. We have Sunderland and we have to go into the game as positive as we can."
Agnew praised the travelling Boro fans after Saturday's defeat.
"They've had a tough season, the supporters, but they always get behind us," he said.
"We haven't won since December so it's been difficult.
"But they continue to support us home and away, and it's something we're all proud of."