There are a number of reasons why the Superannuation File may be higher than the Super Contributions Report.
Super Contributions Report includes negatives
Your Superannuation Employer Contributions Report can include negative values for your employees. However, negatives are excluded from the Super File and will be replaced with a zero. This will mean that your file is more than your Report.
If no further payments are due for the Employee, discuss this with the Superannuation Company or Clearing House directly to receive a refund, as they will not accept negative values.
To amend the super values for the employee, see Process a Superannuation Adjustment
Superannuation File includes values from a previous period
The Superannuation File can include values from a previously processed period if you tick Append Files and a File with the same name already exists in the location you export the Super File to.
To avoid this, you should either after producing the file or before producing the next file either:
Rename the file in the export location.
Move the Super File to a different location.
You can find where the super file will export to by reviewing the Path of Output File on the File Details tab in the File Layout (Payroll, Maintenance, Superannuation, File Layout) attached to your Funds.
If you have already appended the current super processing values to the previous, you will need to either move or rename the file and then re-produce the super file.