I'm a personal trainer who has had a lot of clients use these apps, though not as much these days, so I could be a little out of date.
By far, the issue I, or my clients, ran into is all hell would break loose the moment they would enter their activity level.
The first issue is people way, way overestimate how active they are. For most using these apps, they qualify as beginners fitness wise. One example of an error I would see is while the person may be active, because they're a beginner, practically all their exercise feels hard. In their mind then, they're working out hard, so they're very active, or burning a lot of calories, etc.
In reality though, you're not burning more calories just because you feel you're running, when in reality, you're jogging.
The next issue is the apps use all different kinds of methodology to arrive at a calories burned number. I've had plenty of clients tell me they burned 1,000 calories from their hiking.
Here's a paper for you,
–Constrained Total Energy Expenditure and Metabolic Adaptation to Physical Activity in Adult Humans
Here is the money image from the paper:
What that paper found is there is a plateauing of how many calories you'll burn in a day from activity. No, this does not violate physics. It's fairly simple. You, for example, run a lot in a day. The rest of the day you may be more likely to sit more than you otherwise would.
It's not just voluntary either. In a more extreme sense, if you're a female who runs a lot, your body may start shutting down reproductive abilities to conserve calories. (This is why so many intensely exercising females lose their period.)
More details on the study.
That study has been out for years now. I'm not sure I've even seen it discussed in the fitness community, much less even tried to be accounted for when calculating people's daily calorie needs, nor am I sure that's even doable when you see how much variability there is. (Look at how spread out those dots are above!)
This may be a little off base for your personal situation, if all you've put in is desk job for activity, but the larger point is still there: we've given people an enormously false precision as to how many calories we're able to know they burn per day, from a theoretical model. Even at low activity levels. Notice the very low activity levels in that image above. You can see a 5x difference in calories burned (which was tracked with radioactive isotopes aka a legit method).
The moment you ask the app to project weight-loss for you, you're asking it to project calories burned for you, which is a crapshoot.
The only way to do this is the practical model: eat a certain amount per day (the apps are quite good for this aspect), track your weight -you are your own benchmark- and go from there.
It's still a matter of calories in vs calories out, but the calories out is not straight forward. The body has all kinds of tricks. You might start eating less, but it might start burning less. Of course, at some point, you'll lose weight. Any client who told me eating less calories didn't work, I'd simply respond, "what if I locked you in a jail cell and never fed you?" That usually got the point across.