The root cause of this behavior can vary. Typically, the databases have become out of sync.
It's possible the Raiser's Edge database is a more recent backup than the NetCommunity database. Consequently, there are transactions that exist in The Raiser's Edge NetCommunity Plugin that do not exist in the NetCommunity database. The plugin prompts the transaction to appear as checked out.
If the Raiser's Edge database previously was associated with a NetCommunity database, but then NetCommunity was cancelled or stopped being used for a while, and then resumed, the transactions can show as checked out.
The transactions can be checked in following this article: How to check in transactions.
If these are truly new transactions that are not checked out by the user in question, follow Option 3 - Check in all unprocessed transactions in the article above.