The phrase "special allowances" refers to extra privileges or benefits that someone is given in addition to what is typically provided to everyone else. Full definition
You're going to have to make special allowances for two - player play. (pressthebuttons.com)
Until this change, banks received fees to originate loans plus a «special allowance payment» each quarter for the loans they carried on their books. (gse.harvard.edu)
But instead, they pushed for special allowances on insurance and background checks. (nytimes.com)