About the only "problem" I've had with my '06 is that on a rare occasion while trying to fill the gas tank, it will click off before being full and won't allow anymore gas to be put in. I just drive it another day and fill it up. On average it's only happened a time or two per month the past 2.5 years.
Some have had the parking brake "freeze", windows stop going up/down, factory cd player skip/not play cds...
On the early mustangs, If you invert the fuel dispenser or turn it sideways, it will fill. The auto up/down feature. If it sticks/goes up to the top then drops an inch, just hold the button up or down for approx 5 seconds till you hear a light click. That should fix that. The Shaker 500 is notorious for not playing/not ejecting burned CD's. I don't think they have solved that yet. Other than that there is not much else to worry about.