Ive recently noticed, While my microphne permissions are disabled, people can hear me over the Call, Please Explain How Can i deal with this issue
ive also noticed fdroid starting on boot and checking for updates successfully even tho i have restricted its battery fully and background data as well
Rookie
This has nothing to do which a compromise and you are completely misunderstanding how a compromise would work and which signs it would show (probably none at all).
The first issue you're describing is merely a known upstream bug. Only reason this works is due to the Phone app already being privileged, normal apps still cannot bypass the Microphone kill switch.
The latter has nothing to do with battery background usage. Apps can tell the OS they want to be started on boot, this is separately from the battery restrictions.
Also, you shouldn't use F-Droid in the first place, it is severely flawed, dangerous and insecure. Completely avoid it and its repositories, the same goes for Aurora Store.
Instead of Aurora Store you should just use the official Play Store. It is the most secure and private for Play Store apps on GrapheneOS and Play Services doesn't get any special privileges. Aurora Store doesn't avoid Google anyways and the really minor info that Google gets with sandboxed Google Play it would also get with Aurora Store. So there is no privacy benefit with Aurora in the first place.
For non-play store app, there is Accrescent on the built in GOS App Store. It is the best option in terms of security and privacy to get apps, so always look there first.
For FOSS apps which are published through GitHub/GitLab releases, you can use Obtainium, a feed reader, to download and automatically update those. Note, Obtainium only fetches and installs apps from sources you give it. its not an app store itself.
Always verify apps installed with Obtainium through AppVerifier (it is available on Accrescent).
So general priority order of apps sources (most to least prior):
