NavMesh generation doesn’t work with physics currently. This is a known issue.
In the meantime, you may need to have your physics object begin play in it’s final location, then move it to where it is falling from at runtime and let it fall from there. This will only really work if you know exactly where the physics object will fall, such as a box falling straight down. For more complicated objects, you may need to fully animate their movement to make sure it lands where you want, and follow the same process.
I know it’s not ideal, but we are working to improve the NavMesh system currently and hope to have issues like these resolved quickly.