Misaligned holes?
In this case, my guess is that all the frame parts fit perfectly together,
before the frame parts are painted.
My experience with assembling various two-wheeled vehicles in
a small custom motorcycle shop leads me to the above guess:
paint/anodized/plated coatings will always change the way the coated
part mates-up with or mounts to other parts.
In my tool kit, I still have an assortment of rat-tail files, round files, oval files.
flat files, sharpening stones, diamond stones and an assortment of tapered
steel alignment tools.
In a pinch, different grits of wet-or-dry sandpaper used with different sized
dowels and wood blocks will be a big help for fitting things together.
A Dremel tool is nice too, but because it's powered, it can get you into
trouble faster!
Good luck,
-Steve