Hi @Stathis Askaridis ,
I have tried to replicate the issue and I was able to see the similar behavior. I would recommend you to raise a support with Microsoft Graph, a support engineer will be able to assist you better. you can raise support ticket from aad.portal.azure.com
And currently creating an Onlinemeeting under a specific Team using Graph API is not available. You can raise a feature request here.
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