The Teams Channel UI design causes a lot of confusion for in-thread replies. Otherwise smart people constantly replying in new thread instead of the active thread. I have grown weary of trying to provide guidance about how to use threads.
I think there needs to be more distinction between replying in a thread and starting a new thread.
A colleague suggests this confusion is partly because the individual 1:1 chat threading behavior (single conversation thread) is different than the Channel Threading behavior.
I'm not knocking Teams overall, I love it actually I use it all day long. But I cannot get over how many people fail to respond in the same thread and start a new one. I think it's more likely this UI is flawed than it is that so many technically literate people are ignorant about how to chat properly.
You aren't alone. In our testing I 'fight' that as well. I believe the UI is up for change sometime this summer, so hopefully it will be addressed then. Also waiting for a 'move conversation' feature as well - then at least you could move the reply back into the conversation. Here's how I try to cope until the changes come through:
Chat with the transgressor with the gray haired lady sticker saying 'nag nag' and directing them to fix it - but I only did it for important threads.
If I am part of the thread I'd reply to it correctly, and they'd see that their reply was lost up into the top of the channel.
Also start a new thread so they can see a channel is more like a forum than a chat.