I'm having the same issue. Here's what happened to create the duplicates
The MXD to publish this layer contains about 10 layers related to Roads and Traffic Infrastructure. Here is the REST Service,( https://services2.arcgis.com/CnkB6jCzAsyli34z/ArcGIS/rest/services/OpenData_RoadTraffic/FeatureServe... ) Someone changed the layers within the MXD, I can't figure out what they did but its been modified. A couple of the LayerID's in the mxd have now changed since this service was originally published. Upon finding the issue my first step was to simply modify the Service URL to reflect the new LayerID. What I did was within AGOL in my organiztion I went to the Settings tab of the Layer and modified the Data Source URL at the bottom of the page to reflect the new REST Service layerID. I modified it from this; https://services2.arcgis.com/CnkB6jCzAsyli34z/ArcGIS/rest/services/OpenData_RoadTraffic/FeatureServe...4
To this: https://services2.arcgis.com/CnkB6jCzAsyli34z/ArcGIS/rest/services/OpenData_RoadTraffic/FeatureServe...
because this is what its now referenced in the REST Service because someone did some changes within the MXD and the "Allow assignment of unique numeric IDs for map service publishing" is checked. Maybe someone put in some layers and then took some out. But the numbering has changed sine the initial publishing of the MXD.
BTW, I use the term "someone" because I'm not willing to take the blame, even though 99% sure it was me.
AS soon as I modified the Data Source URL in the Settings tab the duplicate items showed up in our Open Data Site/AGOL listing. Using the Update Index, Update Item Index doesn't appear to have any impact on the duplicates in the item list.
Can you please delete the duplicate items I've listed below:
Bridges
Civic Address Points
