The IRS has made it clear that employers should contact the transportation system to correct the problem. They should not try to provide cash reimbursements, because once the card is furnished, the benefit has been provided. Any additional amounts given to employees would be taxable compensation.
Important Note: Both of my tax books are now available on Amazon! Updated and expanded to cover new and changing tax law, with an e-supplement covering the latest developments from Congress and the IRS to keep you fully up-to-date.