I've noticed this occurs with only some apps. As an example, I'll be using Fritter, Infinity for Reddit, and Vanadium to showcase this. In the following scenario, Fritter will be set as the default app for all Twitter links.
When a Twitter link from Infinity is clicked on, it creates a separate instance of Fritter inside itself (app icon is Infinity's, but the content is Fritter's).
But when it's from Vanadium, it relies on the main instance of Fritter.
I prefer the latter's way of handling links, so I'd like to know how to force all apps to do what Vanadium just did.