In some instances, when attempting to publish an ArcMap document containing map services to Portal for ArcGIS using the MXD to Web map tool, the tool fails to publish it as a web map.
This is a known limitation. The MXD to Web map tool does not support MXD files containing map services.
To resolve this issue, instead of using the MXD to Web map tool, publish the map service using ArcGIS Pro.
Note: Setting the projection is required for publishing where the map projection must match the basemap projection.