For a US company using the accrual method of accounting, if they receive a bill in January 2016 for work done in 2015, I expect they are supposed to report the 1099 income to the biller as part of the 2015 tax year in which they will take the accrued expense. (Perhaps this is incorrect and it is 1099ed in 2016 tax year, but being so, a similar issue can still arise.)
However, if the billing company uses the cash method of accounting, they receive payment in 2016 and will not include the income until the 2016 tax year. How does the IRS deal with this and not end up wasting time auditing the billing company for not having their return's income match the reported 1099 for 2015? Does the cash filer have to somehow clue the IRS in to say why their income does not match the reported 1099s as part of their return?