If you are not fully hosted by Blackbaud, ensure your Raiser's Edge and Raiser's Edge Web Service are on the most recent version.
The most recent versions can be found on downloads.blackbaud.com.

How to check the version of NetCommunity

If you are on the most recent versions and you confirm the transaction in the plugin is a true duplicate, it can be deleted from the plugin. In rare circumstances, cached transaction data may repopulate into the NetCommunity plugin. We see this happens at times with Bulk Processing, though it may happen for single processing as well. Even though the transactions made it into a batch, in the background the database may cached the XML data and send it back at a later date. 

As long as the transactions are confirmed to not be unique, there is no concern over deleting the duplicates from the plugin. 

This behavior can also be prompted by customizations. You may need to consult with a web developer or use the stock donation form in order to deter the behavior.