The common case is considering projects which have one element that is FOSS and another that isn't. For example: ProtonMail, who apparently offer a FOSS mail client. They never presumed to offer mail server software; and FOSS mail server software is available. So a button calling them out for not being really FOSS kind of misses the mark. You don't see an entry like that for, say, GMail - so if Proton did not provide a client at all, they would have faired better.
Another specific case is that of Signal. The client and server are FOSS, but they're designed for no federation, so you can't (?) use a modified Signal client with the vanilla clients, and you definitely can't add a server to the network. This effectively prevents modified versions of Signal from being usable. So, is it really FOSS? The site's verdict is: Unqualified yes, Green button.