The rattly diesel-type sound on start-up.
The water running off the tailgate after I've washed, dried and polished the car and then open the bootlid.
The way the water trickles down the side of the car from the bottom corner of the rear side windows, again after washing/drying/polishing. This affects three door models only and I had the same problem on my Mk 4. I have to stuff a folded piece of kitchen roll in the corner to stop trickles, but as soon as I remove it (soaking wet) it trickles again! I even use Bounty, not some Tesco Value rubbish that doesn't absorb anything!
The flimsy feel of the knob to adjust/heat the wing mirrors. I keep thinking it's going to snap off every time I turn it on a frosty morning to clear the mirrors.
The way the fuel cap doesn't sit on the flap very well and always falls off whilst I'm refuelling. One day it's going to scratch the car. It used to sit so much tighter on the Mk 4 fuel flap and felt more secure.
The front cupholders are a bit naff. With a full bottle of Coke/water etc. it is a bit top-heavy and the cupholder doesn't grip the bottle enough and it topples over when you go round a corner. Again, I prefer the design of the Mk 4 dash cupholders.
The fact that you can't access your drink easily with the armrest slid forward.
Nor the handbrake.
The Edition 30 badge on the back of the car looks too much like a Ford TDCi badge.
Not being able to use the 12v socket with the ignition off. Sometimes I need to charge my phone and used to leave it in the car at times to charge but now I can't.
I think the tilt/slide design of the front seats is pretty poor. I have to explain to passengers to tilt-slide-slide-tilt otherwise they don't go back to the original position!