Thanks, @Spaghetti Monster🍝, for the comments.
We have been using osm-revert in the project for almost a year and have not had issues with it. We investigated this case and it appears a team member accidentally created a node and later split the way at that node. Reverting the node also reverted the way created by that split.

We have added extra checks to our guidelines so the effects of any fixes are understood before they are applied.