After finally getting through to speak with someone, yes this is a known bug. The allowances are not being pre filled at the ATO end. Therefore if staff lodge their tax return and do not realise that the 'allowances' field is blank they will be under declaring their wages.
Reckon have advised that they are hoping to have a fix for this within a week. In the meantime, I would be advising ALL staff that have an allowance to double check or advise their tax agent not to go off the ATO portal.