Howard, who had been taking cover in a ditch, died instantly, the inquest in England has found.
Commander Paul Tremelling told the inquest that the biggest mistake was the pilot's failure to enter co-ordinates for the attack into his onboard computer.
"You would always, always, always put that grid into the machine," the Mail reported him as saying.
He said the pilot might not have done so if he thought his targeting pod was defective.
"In that situation, what he should have done, had he thought there was an error in the equipment, it should have been the first thing he mentioned," Commander Tremelling said.
The inquest also heard that a fault meant the pilot could not share his map with the ground commander, making it harder to be sure they were looking at the same target.
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Commander Tremelling said it might not have been an issue if the pilot and ground commander had established clear markers on the ground so they both knew what they were talking about, which they did not.
It was unclear why the pilot was not aware that friendly troops were within a danger zone of 60 metres from the intended target.
After the fatal strike, Lance Corporal James Appelt, a trained medic who was in the ditch with Private Howard, said it was clear that the sniper died instantly.
"I was desperate to do something but I knew I could not do anything for him."
Coroner David Ridley concluded that Private Howard died as a result of being shot by the jet, but added that communications issues contributed to his death.
"Jack, who had been laying in the ditch just short of the compound along with his comrades, was struck and Jack was instantly killed by one of the rounds," the Mail reported the coroner as saying.
"Whilst the cause of Jack's death was the 20mm round fired from the attacking jet plane, communication issues between the forward air controller and pilot directly contributed to the incident."
After the inquest, Private Howard's father, Roger told the Mail the family was satisfied by the "very thorough investigation".
"It certainly answered all our questions and we are grateful that the coroner devoted time to getting to the bottom of what happened," he said.