I agree with @Bill Presson since the company had the opportunity to review the calculations and it was the company that wrote the checks and took the deduction on their tax return.
The only possibility that this was done in error would be if the plan document has a fixed allocation formula and with no discretion to decide each year how the contribution should be allocated. This is pretty rare these days.
Take a close look at the plan document. The comment that only "certain HCEs" were not going to get the same rate as the owners implies that there different allocation groups among the HCEs, and there is no mention of what NHCEs (if any) received as an allocation.
Has the CFO thought about the employee relations aspect of taking contributions away from participants? One would think that HCEs in general are making substantial contributions to the success of the company, so why create a disincentive by saying the company made a mistake and wants to take back part of their contributions (probably including related earnings)?
Any change from past practice is a decision that should be made by the owners.