Here is the thread in the warranty section on this forum about others, including myself, with the issue:
http://www.fiestast.org/forum/fiesta-st-discussions/5915-climate-control-heater-issue.html
Mine doesn't work properly on manual mode, either. The actual settings seem to vary each and every time I drive the car, but the general idea is that manually setting it from 81-85 blows out barely above cold air, setting it to HI blows out stupid hot air, setting it to 80 or below blows out full on A/C cold air, even if the A/C switch isn't pressed. Sometimes I can start the car and it will work normally, but only for that drive and if I stop/start it again without letting it fully sit and get cold again it doesn't work. Example, I picked my kid up from school today and from home to school, a 3.5 mile drive, it worked. He is in preschool so I have to go to his class to get him and when I turned the car back on to leave, 5 minutes after turning it off, the climate control wouldn't work and wouldn't blow warm air on anything less than HI.
If AUTO didn't work but I could manually control it, I would be more on board with riding it out until an official recall or TSB is released from Ford, but in my case, and many others based on this forum, other forums, and Reddit, manual control doesn't work right either. Leaving it on HI isn't realistic because the car is sauna hot inside 10 minutes and you have to turn it completely off which then makes it freezing cold 5-10 minutes later and windows start fogging and crap. I'm not cool with playing that game every time I drive the car in cold weather. Not to mention, I don't think it's too much to ask for the climate control in a brand new car, economy platform or not, to work right.
What kills me is that people driving '14s and '15s don't seem to have the issue. Aren't issues supposed to lessen as a car continues its production run? How the hell does something like this happen between '15 and '16 when nothing in the car was actually changed and the same auto climate system has been there since day one? My guess is one of the following:
1. Ford got a bad batch of parts and it was used both in new vehicle builds and is ALSO being used for the replacements that aren't fixing anything.
2. Being an automatic system there are temp sensors to judge the outside/inside air temps and I imagine this is monitored by either the ECU, or another computer, and that computer, or programming routine in the ECU, isn't doing its job right and needs to be updated which is why part swapping isn't doing anything.
I just dropped my car off today so I'll see what happens, but reading other peoples experiences on '16 models with the same issue doesn't give me the warm and fuzzies. Like I said above, if my manual control worked normally all the time I wouldn't be so irritated, but for the entire system to not work right and for my car to have 130 miles on it and be in my possession for 4 days before having to go into the shop pisses me the hell off. I'm even more mad because I noticed this issue before I bought it and raised concern, but being a former auto tech I never imagined it would be more than a basic temp sensor replacement or something. Buying the car knowing the issue was there is on me and it's my fault I assumed it would be a quick fix, but the rest is on Ford and I really, really, really hope they devote some engineer time to fixing this.
Side note - I got to sit in a Fiesta Titanium on the lot and confirmed it was doing the exact same thing as my car so I've personally seen it on two vehicles and read accounts from a bunch of people on forums and whatnot that have the issue meaning it is probably pretty wide spread considering how many people never go to forums to talk about their issues.
EDIT:
I also assume this will be an issue in the warmer months because the cold isn't regulated at all, it's just full on freezing. I can't speak for everyone, but I know when it's hot out I'll turn my A/C on max for a bit to cool the car off and then turn the temp up so I don't get hypothermia. If the A/C has one temp setting of "REALLY FREAKING COLD" that's almost as big of a problem as the heat not working right if you live in an area with hot/humid summers like I do because driving without A/C = covered in sweat and driving with full max A/C at all times isn't really a good idea either so you're right back to constantly having to turn it on and off again to keep the temperature somewhat under control.