Assume that you try to retrieve the message tracking logs by using Exchange admin center (EAC) or the Get-MessageTrackingLog cmdlet in Microsoft Exchange Server 2016. You could notice that the Microsoft Exchange Transport Log Search service doesn't index all the message tracking logs that are available on the server. Therefore, you can't retrieve all the message tracking logs that you defined.
This issue occurs because the wrong prefix is returned, and then the wrong IndexPercentage is used while indexing.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.