Is it actually "entirely different", or is it a difference of a few degrees?
Like I said above a couple times, you're not going to catch the apps with the exact same data set because they're all on different caches. When you see the main Apple Watch app update when you open it, it's not necessarily updating its data - it might just be refreshing from data already downloaded via the complication.
The main Apple Watch app also uses a complex algorithm to forecast weather data in between data refreshes to speed up load times instead of finding your GPS coordinates, downloading data from the network, then updating the UI every time, which can sometimes be very slow on the Apple Watch. So, as a simple example, if it's 70 degrees at 10am and it's forecasted to be 80 degrees at 11am, it won't continue showing 70 degrees for that entire hour - it'll be 73 degrees at 10:15, 75 degrees at 10:30, etc. It's still using the same data set as the complication, it's just forecasting out. It's so much faster doing it this way in terms of load speeds, it's ridiculous - and you get much more timely data than you would normally. And it took a ridiculous amount of time to implement on my end. (You can always do a direct refresh of the weather data using Force Touch.)
The main iPhone app doesn't use this algorithm because it doesn't have any delay in finding your GPS coordinates, downloading data, and updating its UI like the Apple Watch does - it's all instant. But for that reason, it's never going to match exactly what the main Apple Watch says.
If you're obsessively checking all 3 displays, then there will always be differences between them. The iPhone will be the most up to date, followed by the main Apple Watch app, followed by the Apple Watch complication. They'll always be within 30 minutes of each other.
In any event, if you're having technical issues please feel free to email at support at meetcarrot dot com.