Oh wow that sucks. This is also the very first time I am hearing of this issue on the E9X platform. It was a common problem on the previous generations.
It would probably be best to remove the headliner from the car and peel back the bubbled area, then apply 3M High Strength Fabric adhesive. Let it cure and then re-install.
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'16 M3 | '23 718 Spyder
Past: E92 M3, F87 M2, E39 M5, etc
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