If it's a 401(a)(30) violation, e.g. they allowed the participant to exceed the limit in that plan (or in multiple plans within the same controlled group), then they have to distribute, as the plan never should have accepted the contribution in the first place. In other words, the plan document probably says that a participant will not be allowed to contribute more than the annual limit, so by allowing the participant to contribute in excess of the limit, there is an operational failure and that can be corrected by distributing the excess under EPCRS.
If it's only a 402(g) failure, and not a 401(a)(30) failure in any plan, then there is no qualification issue and no need to distribute any of the contribution. In fact, there is no ability to distribute the excess unless the participant has a distributable event, such as age 59½ or termination of employment. There is a tax consequence for the participant but that is not the plan's problem.