As Kevin says "upload"???. Reckon does this automatically each new tax year.
You need to check your PAYG settings on each employee whether to have set them to TFT which is normal or No-TFT which will take the higher rate of tax as for a second job. Or even if there is an extra amount or % put in to take extra PAYG
Or even if you have set up Super to have PAYG taken out
1. What tax code are you using for the employee
2. What is the gross taxable amount
3. What is the value of any Salary Sacrifice entries
4. What was the amount of tax calculated.
Without something like this it is impossible for us to see a picture of just what is going wrong which might enable us to pinpoint the error..
John L G