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Can you post the CLI command or API call you are making with the filter included?
Assuming your using ListUser API https://docs.aws.amazon.com/cognito-user-identity-pools/latest/APIReference/API_ListUsers.html#API_ListUsers_RequestSyntax
Please check if you have PaginationToken which might be link to next list of users. An identifier that was returned from the previous call to this operation, which can be used to return the next set of items in the list.
Refer the link above for details.
It looks as though Cognito's ListUsers API returns a sparse result set - according to the Managing and Searching for Users page in the documentation, "ListUsers returns a paginated list of zero or more users. You can receive multiple pages in a row with zero results."
The suggested workaround is to "Repeat the query with each pagination token that is returned until you receive a null pagination token value, then review the combined result."
Note this applies when using the CLI with a client-side filter; it doesn't explicitly state whether the API (and / or SDKs) are similarly affected.
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Which Cognito API are you using https://docs.aws.amazon.com/cognito-user-identity-pools/latest/APIReference/API_Operations.html? I don't see GetUserList API from the list. Is that a function from a library? If so, which one? Also, can you share the code snippet to reproduce the issue?