Dalicon Can you provide us with an example of what these apps are, and exactly what they expect? How does it work on Stock OS but not on GrapheneOS?
Apps being sandboxed is not a feature unique to GrapheneOS (although GrapheneOS improves and hardens sandboxing in multiple ways), so the sandbox is not what's causing those apps to not see each other. Apps in the same profile can communicate with mutual consent, so this is likely how they're doing it.
If you can provide us with more information of screenshots and what the expected behavior should be vs what it is right now, I'd be more than happy to look into this further for you.