phantom empty shape

I’m seeing a phantom empty shape in some glyphs for a new font I’m working on:

This is an older font that’s being converted from FL5->FL8->Glyphs. I exported a .glyphs file from FL8 to work with in Glyphs, and, depending on the letter, am copying either whole glyphs between the two files or just layer outlines. I’m not sure what treatment was done here but there have been a few that popped up now. Can send an isolated file if you’d like.

Using Glyphs v3529.

Can you save, close and reopen the file?

I have a file with this letter isolated, can save close and reopen and it’s still phantomed.

Can you send me the file?