Active Salesforce duplicate rules can conflict with third party integrations that insert records into your Salesforce organization. When the third party product inserts a new record into Salesforce, the Salesforce duplicate rules are run. If a duplicate is found, the record is not inserted into Salesforce and you may not know. Most of the third party products which insert records into Salesforce contain their own built in duplicate matching rules and should be excluded from the Salesforce built in duplicate matching rules.
Best practice is to allocate a Salesforce license to third party integrations and assign them to a profile specifically set up for the integration user(s). This profile can then be excluded from firing the duplicate rules.
There are also some third party integrations whose processes use the user who set the process up as the creator for new records such as the iATS Download Journal. These should be reviewed as well as they may also cause records not to be inserted into Salesforce. The fix is to make sure the processes are owned by a user that is excluded from the firing of the duplicate rules.
In the example below, the matching rules have been configured to run only when the Current User is not equal to our two integration related profiles. This will exclude them from the duplicate checking process.