403(b) and SEP/IRA

[Guest condor]

A 501©(3) organization has a SEP/IRA established fbo employees. The organization funds the SEP/IRA. Employees choose mutual funds for their account. This organization also has in place a employee maintained 403(B) in which the employees choosee the mutual fund investment. The responsibility the organization has is to deduct the contribution from each employees check and send it to the custodian. During an audit, the CPA doing the audit says this is a possible conflict in interest and may violate ERISA. Is this a conflict? When the plan was set up this organization was not allowed to do a SAR/SEP IRA so the 403(B) was chosen. Any help or suggestions would be most appreciated.