A freedom of information request showed £829,000 in overpayments had been made to 210 pilots between 2007 and 2013, because of the administrative mistake.
Some aircrew had queried their rates but been assured they were correct.
The Army said it was considering the debts owed by serving and retired pilots on a "case-by-case basis".
According to an internal audit report, the action to recover sums of up to £30,000 from the pilots and instructors had continued despite officials accepting the money had been taken "in good faith".
The overpayments were said to have been linked to differences in rates paid to pilots, based on their length of service and job positions.
The rules governing how pilots' pay was calculated were described as "complicated and contradictory" in a series of documents published on the Ministry of Defence website.
Administrators were reported to have "inconsistently interpreted" the policy over a period of "many years", with some confusion over the system arising as far back as 2002.
A June 2014 letter to MoD officials also said the Army was "firmly of the view" the debts should be written off due to "compelling" operational reasons.
The Army said a decision to recover the pay must be considered against the "significant risks" that losing experienced air crew and senior instructors "would cause to air safety and the longer term costs of training replacements".
It took four years to train an attack helicopter pilot at a cost of £3.5m, with the cost of training an instructor put at £8.5m.
It was said that 15 pilots were "directly citing the incorrect payment as the deciding factor in their decision to leave the Army".
The issue has also "been identified as a factor in the decision to leave" in other resignations.
The Army said it was not aware of any resignations linked to the overpayments since 2014.
A spokeswoman said: "We have apologised and explained the circumstances of the overpayments to all of those affected.
"In accordance with standard government practice, arrangements have been made to revert their pay to the correct levels and all affected personnel are now receiving the correct pay."
Fifteen of the Army's most experienced helicopter pilots quit in a dispute over a demand they repay wages given to them in error, documents have revealed.