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Why are feature classes in the same database listed under different source groups when using List By Source?
The List By Source method in the Table Of Contents organizes data in an MXD according to the folders or database connection properties. Therefore, if there are any variations in the data, the feature classes are grouped by their matching source, hence the reason why the feature classes are listed under different source groups.
For more information on how data paths are listed in a map, please refer to the links in the Related Information section.