GraphQL doesn't return projects for one particular user

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Summary

I have an OAuth app and I use user's tokens to make API calls. One particular user has the following situation:

I use their OAuth token to make this GraphQL request:

query { 
  authCheck: currentUser { id }
  projects(membership: true) {
    pageInfo {
      hasNextPage
      endCursor
    }
    nodes {
      id
      name
    }
  }
}

And I get a result where nodes array is empty. And if I do the same token to query Gitlab REST API:

GET https://gitlab.com/api/v4/projects?membership=true

Then I get dozens and dozens of projects of the user.

Steps to reproduce

I can provide you with the ID of the user and OAuth app privately.

What is the current bug behavior?

GraphQL incorrectly shows user has no project he's a member of.

What is the expected correct behavior?

Both APIs should return same logical information.