Pakistan went down by 84 runs in the fourth and final day-night international, handing the series to England 3-1 -- their ninth series defeat in 11 since adopting the Gulf States as their neutral venues in 2009.
Waqar said Pakistan started the series well, with a six wicket win in the first match in Abu Dhbai.
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"Of course, the ending was disappointing," said Waqar.
"We started off well but unfortunately we couldn't finish it well. This is a young team and it's a learning curve for them."
England levelled the series with a 95-run win in the second game and achieved a six-wicket win in the third.
Since taking over in June last year Waqar has lost six one-day series which has prompted former captain and coach Javed Miandad to call for his sacking.
Waqar said he takes positive criticism in his stride.
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"When you lose, criticism comes and all the positive criticism has to be worked on," said Waqar who denied Pakistan team is under pressure to qualify for the 2019 World Cup to be held in England.
"I don't think that's a concern or builds pressure," said Waqar of fear of playing the qualifying rounds if they fail to be amongst the top eight teams in one-day rankings on the cut-off date of September 30, 2017.
"You are giving youngster’s opportunity and when you do that in modern cricket, which has become very fast, that takes time."
Waqar said England's Jos Buttler played an extraordinary knock to take away the game from Pakistan in Dubai on Friday.
"I don't think we relied more on spinners, we played one spinner and another was an allrounder. I think without any doubt they played better than us, and the way Buttler played it took away the game from us."
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Buttler smashed 52-ball 116 not out in England's imposing 355-5 - his hundred coming off just 46 balls, the fastest by an English batsman.
Pakistan were dismissed for 271.
Waqar said he was still "proud" of his players.
"The way they started and played well throughout, unfortunately we lost but I think we have gained that mindset which I have been saying that we have to play positive and attacking cricket.
"I am sure they would have learnt from mistakes."
Waqar backed leg-spinner Yasir Shah, who managed just two wickets at 82.50 runs.
"It's a different ball game when it comes to one-days as he takes time to settle," said Waqar of Shah who took 15 wickets in Pakistan's preceding 2-0 Test series win.
"I am sure he will be one of the best ODI bowler in near future."
Pakistan and England will now play three Twenty20 internationals in Dubai (November 26 and 27) and Sharjah (November 30).
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