Are you sure the property is co-owned?  Why did the tenant just pay one brother?  Why did the brother cash that check?  Is there a lease with both brothers' names on it as lessors?  Explain to the one brother that to avoid this problem next year, he and the tenant should be more careful this year.  

For now, how much money is involved?  $800, or $80,000?  If it really doesn't amount to a hill of soybeans, the brother with the 1099 can deduct half of it as rent and no one at IRS will notice or care.  If it's a large amount, then have him file the 1099 as a nominee distribution.  And charge him enough that he has an incentive to prevent the problem next year.