As long as it's just a rust stain on the outside of the glass, and the glass is smooth, I don't worry about it.
I have a few, left over from the days before I learned to remove the rings after canning, that have those tell-tale rust stains. They don't cause any problems.
Your main area of concern is the rim of the jar. If there are any scratches, nicks, rough, even rusty bits from lids adhering, they shouldn't be used for pressure canning. Don't use a scrubbie pad or steel wool on those rims. May leave tiny scratches.
If you want to try to get rid of the stains, my first thought is to try CLR. While I haven't used it for that purpose, a lot of people recommend it.
Hope this helps.
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