"This series didn't go well for us, but not all series will go well for you. The preparation was good but we made mistakes," Pakistan's chief coach said.
Speaking to reporters after suffering an eight-wicket defeat against India here at Edgbaston, Whatmore pointed out the first defeat against the West Indies hurt Pakistan.
"We did well in the practice matches and knew the conditions well at The Oval but we failed to take advantage," Whatmore said.
"Whether we were chasing or setting up a target, we could not score the runs. We lost wickets in clusters and in a short tournament could read the wickets well enough," Whatmore explained.
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Stating that the young bowlers did a good job and the fielding was gradually improving, Whatmore held his batsmen responsible for the Champions Trophy defeats.
"When you lose wickets upfront, you can't do much," he said.
Whatmore disagreed with the fact that Pakistan's batting trend has been worrying of late. The team lost the ODIs in South Africa and continued their dismal run in the UK.
Whatmore urged Pakistan selectors to prepare a squad with 2015 World Cup in mind.
"It's up to them which players they want. The domestic system is quite good in Pakistan and whether players have to play overseas, I am not too sure," Whatmore said.
Pakistan left out veterans Younis Khan, Shahid Afridi and Abdur Razzaq for the Champions Trophy while veteran pacer Umar Gul missed out due to injury.