So I’ve just tried testing my latest font in Adobe Illustrator and noticed something weird going on with the Cap Components as well as Corner Components on glyphs that are made up of other components that have been mirrored (eg: the d is just a b component mirrored). The Corner Components on the original glyphs look fine.
Are the errors also appearing in the Preview pane within Glyphs?
Does changing the left/right alignment on the component fix the issue?
What do your caps and corners look like: where are they in relation to the origin, and are you using anchors?