It could be that the tags that are missing are Subscription tags or Resource Group tags that are not included in the CUR.
FlexReports for Azure only support tags from the Cost Management and billing data provided from Microsoft Azure. Subscription tags and Resource Group tags do not show in the raw bill and therefore do not display in FlexReports. Only Resource tags that are included in the CUR from Azure can display in our FlexReports. However there are a few workarounds available.
Option 1: You can create a perspective that has a group which pulls in assets that have your desired Subscription tag or Resource Groups tag, then in FlexReports you can use datasource "Azure Cost Management (BETA)" and filter by your perspective.
Option 2: You can enable tag inheritance in Azure which would make every single asset inherit the tags that are applied at the resource group or subscription level. This is only a good option if every single one of your cost centers maps directly to a subscription. If not, then go with option 1.
https://learn.microsoft.com/en-us/azure/cost-management-billing/costs/enable-tag-inheritance.