I bought my 05 Focus ST with 14K. Several thousand miles later, it became difficult to shift, especially into first and second after a cold start. Ford replaced the clutch, but that didn't solve the problem. I took the car back, and the dealer kept the car for a week and a half, and finally brought in a factory rep. They discovered a bad shift rod in the transmission, which they replaced, and it has shifted fine since. All of the shift related issues were repaired under warranty and the cost of the loaner was also absorbed by Ford.
Last week, at 45k, the charging light started coming on at low revs. This time I paid $524. for the installation of a new alternator. I'm disappointed that a factory alternator (the controller actually) would fail at 45K.
I love the way the car drives. It is quick, handles remarkably well, averages over 30mpg in summer and about 29mpg in (Maine) winter, and is reasonably comfortable for my 6'2" frame.