Very common for them not to be bang on. It's not generally a problem functionally and becomes a lot less noticeable once tuners and strings etc are on.

The fix is to plug them with a bit of dowel and re-drill the holes, which isn't difficult. The repair is hidden under the machine head and washer so you'll never see it.

I'd say it's probably not bad enough for a replacement, but it never hurts to ask the question if you don't feel like you can tackle the fix, although now that you've started finishing on the neck it's probably not an option.