Cross fingers its fixed. But do a proper professional audit for the future of what you expect, separate from what any applications are reporting. List all the extension numbers that should be valid (users and groups). Then see how the user records and extensions records in SSA/IP Office Manager/IP Office Web Manager match up to that.
And "User don't use any kind of Softphones, ..." - that you know about, including unauthorized users. Users with the right user profiles, if you've got licenses for anything above basic user, can simultaneously connect on a phone and a softphone. User records that are redundant and don't match an extension record can still be used to connect a softphone.
Do an audit and maintain it. Use it to clear the configuration of any redundant records.