Two things to check:
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Be sure you only move or rotate ALL rigidbodies using the Rigidbody API
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Be sure you enable continuous collision on all rigidbodies.
More reading:
With Physics (or Physics2D), never manipulate the Transform directly. If you manipulate the Transform directly, you are bypassing the physics system and you can reasonably expect glitching and missed collisions and other physics mayhem.
Always use the .MovePosition() and .MoveRotation() methods on the Rigidbody (or Rigidbody2D) instance in order to move or rotate things. Doing this keeps the physics system informed about what is going on.
With a wheel collider, use the motor or brake torque to effect motion.