Despite the wonders of jigs and templates and CNC machines and whatever automation magic you can dream up, somewhere in the chain is a human with a brain of squishy meat and the potential to drop a spanner.
Sometimes things are misaligned in the world of guitars. It's rare to fit an after-market pickguard without having to plug and re-drill at least one screw hole. New tuners? Get the drill. Fit a Floyd? Ah, crap.
Misplaced and misaligned bridges happen too. They can cause some serious hassle for the player. That trem in the image above is not going to be the most reliable for returning to tune for instance.
Tun-o-matic bridges can sometimes be found loitering in completely the wrong position too. And not just on Gibsons. This mahogany-body Tele on the right is a cool little Gibson-like Squier. It'd be cooler if the bridge was in the right place, though. Cue the cutting of wooden plugs, the plugging of holes and the re-drilling of correctly-placed mountings.
Wherever possible, it's best to plug holes with the same wood as the material you're plugging. If the plugged repair will be visible, it's nice to match the grain of the surrounding wood as much as possible to minimise signs of repair.
Plugging with hardware-store dowels isn't generally the best route. These are typically made of soft wood and you'll usually end up with end-grain showing in the plug. This tends to stick out like a sore thumb in a repaired surface and is best avoided, if possible.
If you're doing your own plugging, cut your plugs from matching wood when you can. It's possible to increase the size of the hole to be plugged to match the size of your plug. If you go this route, be very careful—drill bits can wander and guitar finish can chip.
Take it slow and easy. Good advice in guitar repair and in life. ;-)
A better plan—if you've got a hole that's a different size to your plug-cutter tools—is to do things the old-fashioned way. Good, honest, whittling.
Cut a long, square-section of hardwood, just bigger than the hole to be plugged and get carving. Knock off the corners over and over until your four-sided section becomes eight, becomes sixteen, etc. A good, sharp chisel will give you better control than a knife. When you're almost round, switch to sandpaper. A good fit is important, so don't be tempted to go with something too small.
Go, my friends. Go and plug with confidence.