The app uses Cal (in the activity summary specifically). This is a non-scientific unit that has caused great confusion and even damaged the ability to communicate precisely and even scientifically, because Cal is pronounced exactly the same way as the very different scientific unit cal.
The correct unit is kcal, and while this used to seem like a lost cause, it’s actually gaining a lot of momentum recently. A company as big as Wahoo should be getting it right.
I snorted a little there, not because I disagree with the sentiment or the suggestion but because there are many MANY things that The Company ought to be getting right but still haven’t 
My guess is that most people that use SYSTM and the other Wahoo apps aren’t scientists and I’m betting, like me, they treat cal/Cal/kcal interchangeably. I don’t know anyone who actually uses the term “cal” as it’s defined and always just assume they mean kcal.
The point really isn’t to appeal better to users, but to be a good citizen and help to make the conflicting (not merely incorrect) usage disappear. There’s a tiny risk that some users will actually be confused by kcal, but the worst thing that results in is that they either wouldn’t care, or would learn, but kcal is becoming quite common.
Garmin uses Calories, Strava uses kJ, Apple Health offers options of Cal, kcal, or kJ.
Honestly, I’d be surprised if The Company started using kcal given the looooong list of things they ought to be getting right 
If you want it done right then surely it should be kJ thet you’re asking for. Joules is the SI unit for energy, not calories.
Calories are obsolete:
I told that exact thing to the donut I just ate and it laughed in my face
There is a convention where Cal = 1000 cal. Capitalized Cal means kcal.
Calories (and I mean calories, see the problem?) are not SI but neither is truly fair to call them obsolete or non scientific. Many very important scientific papers that will remain foundational forever (historical or not) use calories, and they are absolutely something any chemist must know and be able to communicate and work with. You’re correct that kJ is better yet, and is SI, however then one must clearly specify that metabolic energy is being stated as opposed to mechanical output. In cycling kJ is usually used to measure mechanical output and kcal is usually used to measure total energy output of the body in any form (mostly heat). Yes, the most scientific way possible is to use kJ and clearly label exactly what is being stated (which is always the scientific solution), but kcal is still perfectly correct and will cause less confusion. I’m not on this for religious adherence. Practicality is still good too. Conveniently, kJ of mechanical output happens to almost equal kcal of total energy production, by accident, so it’s almost moot, but not quite.
Cal however (and this time I mean Cal, not cal) is an abomination started by the food and health industry that is not only unscientific, but interferes with scientific communication, and it is being phased out, as it should be.
There are lots of bad habits in the world. This is one. Capitalization is a horrible way to indicate kilo, and goes against both science and English and doesn’t solve the fact that the term calories capitalized in many scientific papers and does not mean 1000 calories. The first word of a sentence is capitalized, the first word of titles in these post is forced to capital, (the reason I added “it’s” to the title), every other metric (Distance, Duration) on the activity summary is also capitalized, and caps are not pronounceable. Look at the first sentence in my post, not clear right? This “convention” was invented as an apology after the fact for originally just using cal/calories to mean 1000 calories in the food industry, which is just obviously dumb and harmful. Technically, as a short-form unit only, not a word in a sentence, the caps distinction could be called legitimate (if actually backed by scientific consensus, which it isn’t), but in reality it doesn’t clear up the confusion even in that use, let alone do anything at all to clear up the wording ambiguity.
Again, the point isn’t that all or even any users care. The point is that maybe in a few decades the confusion won’t have to exist at all. Those old scientific papers are never going away. The disruptive use of Cal can.
In principle these are not the same things. kJ that Strava uses measures mechanical work output not total energy production, and that’s actually what we really measure of course, except in the case of HR-only measures, that don’t measure anything well, but at least in theory are founded in correlations to actual metabolic output, although in practice that may have been estimated using cycling measurements too.
It’s possible that if you change from kcal to kJ in apple you get a slightly different value, but I’m not certain. As it turns out (and said above) the conversion factor from kJ or mechanical output to kcal of energy expenditure happens by accident to be almost 1, and within the uncertainties on human efficiency it can just be defined as 1. Really the reason to use kcal is to communicate to people that this is appropriate for comparing to food intake. Apple uses Cal for people who want it. I think it’s too bad they felt the need to do that AND use kcal, but I get it. Many restaurants now even use kcal and it doesn’t seem to be melting people’s minds.
So, when I eat a gel that has 100 calories, does it mean it actually has 100 kcal or 100 000 calories?
Dumb me is now confused …
I “cal” in common usage = 1000 calories = 1 kcal so the gel with 100 “calories” has 100 kcal or 100000 calories.
Tl;dr: yes
These are the same thing.
1000 calories = 1kcal = 1 Calorie
And that’s the point. So, initially the food industry just said 1000 calories is the same as 1 calorie, which is obviously, uh, “what?” Then they sort of apologized and said ok the unit (not word, units are the abbreviations that come after numbers) Cal =1000 cal, and said the words should be that one large calorie equals 1000 small calories or 1000 calories. But of course it was as bad solution and too late. Very often you just see the use “calories” to mean large calories, and very often people try to capitalize the word (not unit) to distinguish, but that’s just unworkable. You basically never see anyone write “large calorie” ever. Rarely you do see “food calorie,” which is the same as a large calorie.
The bottom line is that in any consumer context whatever it is, it always means kcal, and it should just be written that way, and that’s why many places are switching to this.
Almost, technically it is supposed to be:
1000 calories = 1000 small calories = 1000 cal = 1 kcal = 1 Cal = 1 large calorie = 1 food calorie.
Calorie is just the capitalized word “calorie.”
There is a difference between words and units. Capitalization of words is the realm of English, not unit conventions. But in popular casual use the distinction is lost, and practically you’re not wrong. Ambiguous as it is, you do see people capitalizing the word calorie as a casual indication of large calories.
As far as capitalizing units, there’s some precedent, but it doesn’t generally build on the same actual word. C and c are Celcius and the speed of light. kB and kb are kilobytes and kilobits, again, at least not the same word (and let’s not get into the 1024 fiasco)*. There is the large ton and small ton relating to British and American, but they are only a bit different and only because neither ever was really scientific.
*And even these come from industry/computer-science(IBM probably), not natural science, and they do also get confused often since, unlike c and C, it’s always possible to express a quantity using either.
You forgot the metric ton and the s*%^ ton. 
…and over here in Europeland there’s also the tonne and s*%^ tonne, aka an absolute metric s*%^ ton.
Think we probably need the obligatory XKCD reference…
Over 40 years ago when I had my first real science class The instructor gave us a short course in understanding the language of science and the big one he always pushed was always state your assumptions. And this is the difference between the science / technical world versus everyday speaking language. We don’t speak normally using explicitly stated assumptions. All kinds of things are implied and buried in the language when we are just talking.
So while I agree with you I’m not sure the everyday public it will ever be ready to speak or use scientific terms very well. Especially things like calories which already have so much b******* around them.
Many places display kcal correctly now, and the public has not seemed to be super confused by that. Wahoo talks the scientific talk. I don’t see them saying “we won’t talk about glycolysis because the public can’t handle scientific thought.” They can get this right.