When a large number of memberships is supplied in the auth token the individual groups are not provided anymore. Instead a Graph URI is provided. By following that you should be able to retrieve all group memberships for the user.
AFAICT the limit is 150 for SAML requests and 200 for JWT requests.
A workaround on the Azure side is to configure your application for specific groups only and set the groups claim to only return groups assigned to this application (as can be seen in the screenshot here), but it would be nice if this could be handled by this framework as well by following the Graph URI provided and parsing its results.
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