If you need to find your Data Extensions that are Populations, these can be found in Contact Builder > Data Designer > Populations. This would need to be done in all Business Units in an Enterprise 2.0 account. If there are Root Data Extensions in the account, these will not show up in the Populations screen. One way for users to find all of the Data Extensions within a single MID that are either used as a Population or a Root would be utilizing this API call. For the resource, you can pass this to get all of the objects back in a single response:
https://www.exacttargetapis.com/contacts/v1/attributeSetDefinitions?$page=1&$pagesize=500
From there, you would parse out and find all Attribute Sets (another name for Data Extension in this context) with an isRoot property of True. These would be the Data Extensions contributing to the count in the Contacts Counts report. This would need done in every Business Unit of an Enterprise 2.0 account.
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