Can you please try to import the alembic file again, but this time using “Constant Topology Optimization” enabled? This often fixes these issues.
I would try to do a full clean import of the alembic also, instead of possible reimport.
I am not aware of anything you can do to prevent this.
We will see if always enabling this option is a safe thing to do, and if so, we will recommend to always enable this in the docs.
Also not sure what causes this. I think it sometimes might reorder some vertices as optimization or so. And that then causes it to calculate the deltas incorrectly as it picks the wrong vertex on the target mesh.