Datasets with same filename are pointing to a geoserver layer.
In order to fix this problem, there are two ways.
1. update the layer name with unique id
OR
2. geoserver generates with auto-incremental numbered layer name; we need to find out the auto-generated name. Currently java library we are using doesn't return the auto-generated name.

For #1, we need to develop a way to update entire geoserver layers and metadata stored along with datasets.