The emoncms-node-red node simply uses the HTTP API. On a busy RPi I have seen node-red ‘lockup’ so miss or not do things quite correctly. All I can think is the API call is malformed in some way so causing the duplicate inputs.
How is the data getting to node-red before you send it on? Is it possible the data is corrupted or incomplete (I had an issue with sending NaNs at one point).
Final question, are you using the fulljson format (i.e. a valid JSON string)?