In a practice known as "backdating", staff are given options to buy shares at a cheaper price than the current market price by making it appear that the transaction took place at an earlier date when the shares were valued lower.
Stock options increase in value as the market price of a company's shares rises above the "exercise" price at which the employee has the right to buy them.
Backdating the options to a time at which the share price was historically low can provide a bigger profit.
Backdating can be illegal if the process is not disclosed to shareholders and can result in regulators imposing fraud charges.
Apple did not say whether the irregularities it referred to involved backdating.
The options in question were issued between 1997 and 2001, and include a batch that were given to Mr Jobs, although he later cancelled them without receiving any financial benefit.
