Consider the case where bases are loaded with 1 out, and the batter gets a base hit to the right. Runners on third and second score without a throw. But the runner on third missed home while picking up a bat and never touched home. The runner from second touched home and time was called. What should the call have been?
Physically, it doesn't appear that the trailing baserunner passed the leading one, so there's no penalty for "passing a preceding runner..." 5.09(b)(9).
There's less than two outs, so the trailing runner will score.
The lead runner missed home, so can be called out and run removed if the defense appeals.
Might be interesting to think about what would happen if the runner from third tried to go back and touch the plate after the runner from second has already scored. I can't find anything in MLB rulebook that would prevent it. But high school NFHS rules are explicit that a runner cannot re-touch after a following runner has scored.