I'm having this same issue. It's quite demotivating that an app which is supposed to help keep you motivated, is telling you that you didn't work out when you did indeed work out. The other day I just played my workout video again and didn't work out simply so it would record.
For what it's worth, I initiate workouts through the fitness+ app on my apple tv, then I activate it through my watch. Most days, the fitness+ app on my phone records the workout on my custom plan. But at least once a week there is a breakdown and the custom plan shows I missed a workout when I didn't.
As of today, all my devices are up to date. I don't want to reach out to Apple support because all they do is tell you to hard reset everything which is a huge pain, they never try to solve the problem. I embrace the Apple ecosystem because their software is stable and everything is supposed to work. But more and more cracks are starting to appear. I will likely start migrating off of the Apple ecosystem slowly but surely. At least with a system like google or others, I don't have the expectation that things will work properly.