Overlapping shapes don't show up

I have a glyph with overlapping shapes and one particular shape that doesn’t show up. The path is a lighter grey and when I go into the hand view there is no record of this shape. I have attached some screenshots that hopefully explain this.

Can you run the Correct Path Direction command? Otherwise check that there are no duplicate paths on top of each other.

There was a duplicate path, thanks!

I highly recommend the plugin “Show Angled Handles”. It will highlight all sorts of issues, including duplicate paths. You can find the plugin in the Plugin Manager.