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If the holes bother you you can fill them with very short bolts for now or try to use them for something else like make a shelf or tool holders.
I have plans to modify my older UDS and it will leave me with 4 holes, I am going to try and use them for 2 small shelves.
Question: Can you notch the cook grate slightly so you don't need your extra set of holes? Or, it may be a little bit of a pain but to get to the lower grate, can you drop one side down lower than the pins and then bring the other side up so it hits both upper pins? Does that give you enough room? (did that make sense? I'm assuming you have only 3 pins per grate)
Everyone hates making mistakes, but one thing is certain, we humans do make them from time to time. Don't let perfection be the enemy of good (Voltaire..maybe)
Besides, if you are able to re-purpose the holes for shelves or whatever, you can tell everyone you designed it that way.
Notching the cooking grate was also going to be my suggestion. I cut one of the 3 bolts a little shorter than the other 2 help on mine.
Or moving them and adding some hooks like the others have suggested works too!
And we've all made mistakes! If you turn it into something else, no one will ever know. (Except all of us here, lol)