He won't know what its supposed to look like! & over the years he may try to figure out the mystery!!:)

It bothers you enough to ask here so I'd fix it if I were you. But take a day off from working on it so it doesn't feel overwhelming to you. If I feel like rushing something, I force myself to take a day off so I know I'll be satisfied with the finished result. I don't make 'perfect' quilts, I can't seem to piece things precisely so I do my own crazy thing. But if it bugs me, I fix it.
Do what makes you happy!

I am sure we have all tried to fix a square problem after the quilt top has been finished (before quilting/binding). It is possible to take out the 2 misplaced squares and reposition them but oftern putting them back in place is not very easy and will leave uneven seams and more of a mess then if you had left it alone. Show us a pic!!!!!

The boy will never know it but you always will, for that alone, I would fix it.

I think it will take less effort to fix it and have the peace of mind knowing you did your very best, than it will to continue to have it niggle at you for a long time. Sort of like doing something right whether someone sees you or not.

I have fixed similar mistakes of this sort at this stage. If it were already quilted, I'd probably not bother, but under the circumstances it isn't all that difficult to take out a patch or two and re-insert correctly, and you will be glad you did. Of course, if there's some reason to hurry that we don't know about, it's probably something that nobody but you will care about. In that case, think of it not as a mistake, but just a little personal quirk that proves it was made by a person rather than a machine. In either case, just remember that you have already invested a lot in the quilt. It is time to decide one on way or the other, and if you let it go as it is, let it go emotionally, too. I happen to feel there are a lot of things that are well worth doing even if they do fall short of perfection.