Is your auditor saying that the MLO number needs to be on the application when the customer fills it out? Or are they citing you for not adding the number after the application is assigned?
If the former--there is no MLO number to include because you don't know who it will be assigned to, nor has anyone acted as an MLO under the SAFE Act.
If the latter--they are probably citing you under the Reg Z compensation rule where the MLO name and number is required to be listed on the application along with the bank name and number.
Have a conversation with the auditor to find out for sure though.
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I can't herd the cats anymore, so I just set up the electric fences and let them fry when they stray out of bounds.