A schema package requires that all layers reference data from the same geodatabase.
Solutions
In
the ArcMap table of contents, click
the List By Source button 
to group layers by geodatabase. You have the following two options to resolve this
error:
- Create one schema package per geodatabase. You select all the layers listed under each geodatabase, and create a schema-only layer package.
- Copy all data to a single geodatabase and update the data sources of all layers to reference data in the newly created geodatabase before creating a schema-only layer package.
More information
Schema packages are primarily used to share best practices related to geodatabase design and visual representation of data that includes aspects layer properties such as symbology, scale, and so on. To avoid any issues with inconsistent spatial references (after unpacking the package) that could arise if data is distributed across multiple workspaces, schema packages require that all layers reference data from the same geodatabase before creating a schema package.