I tried this in Blender 4.0 and 3.4 and started new projects and the issue shows up in both. It didn't happen for a couple of spheres for some reason and it doesn't happen to duplicates when I duplicate the ones that didn't glitch out. I'm at a loss here and I haven't seen anyone posting about this exact issue. The sphere has multiple modifiers on it but the cube only has the mask modifier on it in my examples.
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By default the Mask modifier will mask the whole mesh except the selected group. If you haven't selected any group it will mask the whole mesh. You can invert the masked vertices with the Invert button though, so in your case just click on this button:
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