When an app has multiple targets with the same platform, e.g. an „App“ target an an „AppKit“ target and both include the same framework, then Accio currently adds only a single framework to the group properly. It seems to try to add a second link, too, but fails - Xcode is placing the second under „Reconstructed Links“ (or similar).

A workaround is to link the frameworks manually, Accio correctly handles them on updates from then on. But Accio should link them correctly in the first place.