Bewildered - MYOB and STP reporting for June do not match even though EOFY finalisation was correct.

I did the 2024 EOFY finalisation process and everything between MYOB reporting and STP matched.

Now I have just done the reporting for the June BAS and have discovered a discrepancy. 

There were three pays entered on June 6, 2 of these are the problem.

One pay was for an employee for their final pay, I did it separately. The amount in STP matches MYOB and what the person was paid.

The other pay for some reason includes this single pay again. The person was paid correctly but there is this double up in STP reporting. And they only got paid once.

1. How did this happen?
2. Does this mean that this employee has been given an incorrect income statement for 2024 FY?
3. How do I fix this up?

Any help appreciated.