Georginio Wijnaldum found space behind the Boro backline to lash home the game's opener just moments before the break.
Boro had defended resolutely up until that point, with Patrick Bamford seeing his claims for a penalty turned away, and Agnew says to go in a goal behind was a big blow.
"We just needed to see it through to half-time and unfortunately, we couldn't do that," Agnew said.
"We had been pleased with our organisation behind the ball and we'd limited Liverpool's opportunities.
"It's moments like [Patrick Bamford's penalty claim] that we work for in these kind of games, and unfortunately it's not gone our way."
With the Premier League season now wrapped up, Agnew says the work begins as Boro look to respond to relegation and plot a route back to the Premier League.
"The season has finished now and we have to reflect on why we've ended up in the position we have done," he said.
"Decisions will be made as the summer goes on. It's about the football club and doing our best to prepare for a big campaign next season.
"There's some really good players and top professionals in the dressing room.
"It was only 12 months ago we achieved promotion to the Premier League, and there's a core group who are determined and will do their very best to achieve that again."