During Exchange 2010 times for one of our Clients some users had special quota set for multiple users that was different than what was default settings in the database. Upon migration to Exchange 2013 and with no space problems the default quota was expanded for everyone making sure everyone has enough space to hold everything. However since some users had their personal quota set that required a fix. Since Exchange 2010, Exchange 2013 and lately Exchange 2016 has that covered with simple PowerShell it's very easy to do this in one go, rather than going one by one thrue Exchange Admin Center (ECP) interface.
Solution
To find users that have non-default quota settings on their mailboxes one can use this very simple PowerShell command
get-mailbox -ResultSize Unlimited | where {$_.UseDatabaseQuotaDefaults -ne $true}
To fix all those users one can simply expand on that command
get-mailbox -ResultSize Unlimited | where {$_.UseDatabaseQuotaDefaults -ne $true} | Set-Mailbox -UseDatabaseQuotaDefaults $true
After executing this and rerunning check again there should be no data returned.
get-mailbox -ResultSize Unlimited | where {$_.UseDatabaseQuotaDefaults -ne $true}