Pakistan beat Bangladesh in a thrilling final by two runs in Dhaka on Thursday, lifting the Asia Cup for the second time.
It was Whatmore's first assignment since taking over earlier this month.
The former Australian batsman – who guided Sri Lanka to the World Cup title in 1996 – said his team had been consistent and competitive in all matches.
“It would have been the icing on the cake to have beaten India and go on to win the cup. We made some mistakes but were in the game late in the second 50-over block,” Whatmore told AFP.
“It was just one of those games that makes you analyse more.”
India's Virat Kohli smashed a career-best 183 to help India chase down a daunting 330-run target but India failed to make it to the final.
Whatmore, who also helped Bangladesh reach the latter stages of the 2007 World Cup held in the Caribbean, praised the Asia Cup hosts.
“Bangladesh had a really good Asia Cup. On the evidence of this tournament, everyone would agree they have improved. They need to be consistent now,” he said.
Whatmore backed Misbah-ul-Haq after the Pakistan captain came under pressure over the team's 4-0 whitewash against England in a one-day series last month.
“I wasn't aware Misbah was under pressure prior to the Asia Cup. He has some wonderful qualities as a captain and contributed well to our overall performance,” said Whatmore, who played seven Tests for Australia.
Pakistan's next assignment is a tour of Sri Lanka starting in May before taking on Australia in a five-match one-day series later in the year.
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Dave Whatmore is right.Had Pakistan beaten India and gone on to win the Asia Cup it would have been a magnificent achievement.In spite of Pakistan scoring 330 runs India were able chase that score successfully.The factor that played a pivotal role in that match which enabled India to win was that they had the advantage of batting second.Unlike in the first session when stroke making is difficult due to slowness of the wicket,in the second session owing to the dew factor wicket became easier to bat on as the ball skidded on to the bat nicely enabling the batsmen to play their strokes.Bowling on such a wicket was dreadful.Slight error in the line and length was costly.India faced this bitter experience when they played Bangladesh,who playing second could overhauled India's score and won the match.Hoping to repeat the performance,Bangladesh having won the toss in the finals elected to field.But Pakistani spinners hampered their bid to victory.