Hi there, thanks for your message.
I have seen one other user report an issue with 3-button navigation recently, but the issue was slightly different to yours. To the best of my knowledge, neither issue seems to be widespread.
The gesture and 3-button navigation functionality comes upstream from AOSP, and to the best of my knowledge it is not changed by GrapheneOS.
Does the issue persist after device restarts? Would you mind confirming your build number in Settings > About phone?
Do you have a GitHub account? If so, you could open a new issue on the OS issue tracker: https://github.com/GrapheneOS/os-issue-tracker/issues.
If you report it there, the development team will see it, and could then have a look if there's anything they can do to help.