Yeah I get the same issue when using Orbot "VPN mode" and wirrguard simultaneously. Seems like an android limitation.
If the app supports orbot by itself (Molly, SimpleX, amethyst) the issue is gone.
Is there a way to use TrackerControl with Orbot at the same time on GrapheneOS? It looks like they're both unable to occupy, at the same time, the one VPN slot that the system provides. https://f-droid.org/packages/net.kollnig.missioncontrol.fdroid/
Discussion
That's a good idea - Tracker Control should support Orbot