I have published an MXD with six layers. When I view the service via the REST endpoint, it lists all six layers (0) through (5) under the MapServer link, but under the FeatureServer link it only list four of the layers. (0) and (1) are missing.
All six layers are SDE feature classes located in the same Feature Dataset.
If you have access to the server log, please check. it should have information about why the layers are not listed in feature server. Most likely the symbology used is unsupported (eg: symbology based on multiple fields)