Travel allowance and STP

My ATO prefill for July and August have been wrong according to payroll totals report.

I will do a file replacement once I can find what is going wrong. I have a phone allowance that is showing as other allowance and I have it included in gross pay ( tax paid on it) and I want it to show as wages in payroll totals not gross. Same as the travel allowance which I have set up as no tax payable and not having it show on payment summaries. It is showing in gross not wages and when I export and upload the gross total is sent to ATO