To add that the folder "Elementary flows" is specific to the openLCA reference system, so that flows inside usually stem from openLCA. If there is folders without "Elementary flows" as the main folders, this is usually folders and flows that were imported as they are or that did not got mapped.
There is no "Elementary flows" folder in ecoinvent or EF or other databases, so they would simply store it in "Resource/XX" instead of "Elementary flows/Resource/XX".
Maybe you have imported some data sets from a source somewhere without considering mapping the compartments and the elementary flows to the openLCA or ecoinvent LCIA methods?