I am seeing this too. Hard to tell whether it's by design or a bug. I'd call it a bug (or at least not expected behaviour).
From what I can tell App navigation links are references by name with a global name space, which means you cannot have two app links with the same name, even if you try to create them in two different apps.
Furthermore, if you create an app link called Link1 in App1, then create a new App2 - the Link1 will not be visible in App2.
Which is bad, as it means it's not possible to share app links between apps.
I've tried customising the security rules to make app links show up in more than one app, but no luck so far.
“ODAG links are meant to be managed similar to Data connections, where a connection created in one app can be used in other apps. However, while the QMC provides a Data connections tab to list down all connections and control related ownership/ permissions, such management GUI is not available for ODAG links. R&D is considering the ODAG link management page in future releases of the product.”
Riccardo Schillaci BI Technical Analyst Datawarehouse & Business Intelligence