If the employer guesses wrong and retaliates against an employee who engaged in no protected activity, that employee might still be able to pursue a claim for retaliation. The protected activity only needs to exist in the mind of the employer to make the employer's retaliation unlawful. However, in our experience, the employers usually guess right.
They can match information derived from the government investigation with a list of employees who:
had that information, and
are known to have enough backbone to speak up about compliance issues.
In most workplaces, this list is unfortunately small.