Microsoft is working on a new feature that should prevent users from starting a new conversation when they intend to reply to an in-line thread in Teams channels. A member of the Microsoft engineering team noted on the UserVoice forum that the company is internally testing this feature.
A Teams channel can contain multiple conversations happening at the same time. When users need to discuss a topic or idea with their colleagues, they can either start a new conversation or reply to a conversation. While messaging functionality isn't something new, some people usually reply in the primary message box for the channel instead of in the reply message box for the thread. It's probably because these two boxes are pretty much closer to each other which could be confusing especially for new users. Probably, Microsoft aims to address this common problem by introducing this new capability in Microsoft Teams.
At the moment, there is no ETA on when to expect the new functionality in Microsoft Teams. The initial user request appeared in May 2017, and hundreds of people have commented on this post since then. The idea has been upvoted by more than 9,000 people until now, and you can also vote on this feature on the Microsoft Teams Uservoice website if this is important for you.