Waiver of penalty for late filing of er1 returns

One of my client is having two excise registration numbers for two different premises. one for manufacturing and one for dealer. They have filed ER1 return of manufacturing activity in time but wrongly they have their dealer registration no. after realizing the mistake, they have filed manufacturing return with correct registration no. Now excise officer related to manufacturing activity want to consider those return as late filed. I wanted to konw , is there any provisions under central excise rules which authorize commissioner to waive off such late fees
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In Central Excise having provisions in this regard but only in the case of issuance of show cause notice, various case law in this regard. But one thing I could not understand how can file the mix dealer return and manufacturing return both format is different and does not tally with each other information.  

Thank you for your feedback. They have not filed their dealer return. Mistake happened while filing manufacturing return and they have used dealer registration number in manufacturing return form and uploaded accordingly . Can you please tell me exact rule no or section number which authorize the officers for waiver of such penalties.

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