I'll add a few:
1. Faded yellow instrument bezels. Have them rechromed, or at least get some silver touch up paint. The same follows for the instrument/gauge needles--paint them back their fluorescent orange color. After 40+ years, nearly all of them are at least a little faded. This is what you're going to be looking at 90% of the time when you're driving the car; why not fix it?
2. Non-original seat belts on an otherwise very nice interior restoration. It just irks me to see generic, one size fits all belts. 3-point belts are fine, but retrofitting aftermarket lap belts in place of original Ford belts just screams cheap to me.
3. So-called "Shaker" cars outfitted with a Torino shaker.
4. Cheap black plastic wiper blades attached to a car that never came with them new. This is especially obvious on a car that has stainless or chrome wiper arms.
5. Incorrect or poorly added options, especially things like window slats and spoilers. If you want to add it, fine, but don't just throw the stuff on the car without researching proper measurements, what kind of hardware it used originally, etc.
6. No sound deadener or seam sealer in the trunk. I see this one all the time. People spend hours making the trunk look great, only to leave the sound deadener or seam sealer off during the repaint. Quarters are supposed to have asbestos-based sound deadner on the portions visible in the trunk. In the seams and around the wheel wells, seam sealer was sprayed, and often not very well. Anything is better than nothing; at least make some effort!
7. People that have partial quarter patches installed, and leave the weld lines. I've even seen cars where the welds weren't ground down on the inside of the trunk. I thought the whole point of repairing a panel was to make it like new?
8. Poorly installed/sagging headliners. This seems to occur a lot with any year classic Mustang, probably because headliners are so aggravating to put in these cars. Very rarely do I see a car at local shows that doesn't have either a sail panel flopping down (especially on '69-70s), or inexcusable wrinkles in the headliner itself.
9. Hacked up package trays. If you want a modern stereo, that's fine. But don't blatantly hack up the package tray with obnoxious speakers! Even worse, the guys that cut the trap door to install speakers, that's pure blasphemy!
10. Blacked out hoods that either have the dimensions wrong, are too shiny, or use some other kind of paint that looks nothing like what Ford used originally.
11. Leaving the steering wheel alone while restoring the rest of the interior. How can people restore every last detail of their interior, only to top it off with a worn and cracked original steering wheel?
12. Getting the interior colors wrong. Either the paint is too shiny, fills in the texture, or is just flat out the wrong color. Lots of people fog everything one color on black interiors; few realize that certain pieces should be charcoal black as opposed to the regular interior black.
13. Mach 1 stripes that are anything but straight down the side of the car. I've seen them going uphill, downhill, and everything in between. If all else fails, break out the tape measure.
14. Incorrect exhaust tips. This is especially aggravating on the cars that have valence cutouts for the specific tips the car came with originally.