Multiple payments can be generated for each pledge/recurring gift depending on the transaction due on or before date specified at the time the transactions are automatically generated.  To prevent this:
  1. In the Batch, select Tools, User Options
  2. Select the Batch tab
  3. Under Default batch information, highlight EFT options
  4. Unmark the checkbox for 'Allow multiple EFT transactions per pledge or recurring gift'
  5. Click Apply
  6. Click OK
Refer to How to include only one EFT transaction per pledge or recurring gift (BB185114) for additional information.