Hi @georgimatev-2532,
Hope you are doing well.
I tried Graph API endpoint messages as shown below.
Also I checked graph API endpoint messages as shown below.
In my tenant I could able to see correct count for mail items in all mail folder. I am unable to reproduce this issue in my tenant. Could you please verify again count of mail in all mail folder such as "Inbox" , "Sent Items" etc.
I would recommend you to raise a support case with Microsoft Graph, a Support Engineer will be able to assist you better. You can raise support ticket from admin.microsoft.com.
Hope this helps.
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