Cant say Ive seen this one before however in the past when you are having issue with bounty acquisition from the companion app signing out of the app completely then uninstalling (followed by installing and signing back in) the app seems to fix quite a few issues. I would try that and see how you go.
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Appreciate the idea. I tried changing characters, crashing the android app, and signing out of destiny to no avail. Got it working again when I restarted my PS4. Something persisted through my session until I restarted. Seems like it's on the game-side, surprisingly.