From the details you provided, most probably, you have some resources (like submaps, topics, or any other resources), external to the main DITA Map folder.
To better notice if that's your case, if you have resources outside of the main DITA Map folder , you could open the main DITA Map in the DITA Maps Manager view and then use the "Validate and Check for Completeness" tool from the view's toolbar. Make sure that, in the validation tool, you set the "Report references to resources outside of the DITA Map folder" option.
It is known that the DITA Open Toolkit has some issues processing this kind of external resources, but there is a simple solution that you could ma use of. That stands in placing the .ditamap file that corresponds to your main DITA Map (which referrs any other submaps and topics) in a parent folder (a folder that would be on top of any other folders that containt the rest of the resources)
You can find more details on this approach in this section
from the Oxygen User-Guide.
I hope this helps.