Did the record keeper require a form along with the funds? If so, it is likely to include language certifying that the funds are from a source that are eligible to be rolled into the plan. A participant signature on that form should end the issue.
From the original post...
---Document calls for any employer allocation to be reduced so as not to cause "the annual additions to exceed the maximum permissible amount".
Put another way... if the plan is a 401k, and at least $5,500 has been deferred, isn't the "maximum permissible amount" for a catch-up eligible participant $56,500?