When you are viewing a message thread (i.e. it is open in front of you, even you typing a message to it) new messages coming to it will only be marked as read if you open the channel again. In detail:

1) Have a message thread open in the app. You can also be typing a new message to it.
2) Somebody else posts a message to the thread.
3) The channel is now marked as having unread messages (its name being in bold). This is despite you reading the message (it appeared just where you're typing).
4) The only way to get rid of the notification is to open another channel, then open the original channel, and open the message thread (which has other issues, see: https://microsoftteams.uservoice.com/forums/555103-public/suggestions/35527471-make-it-easier-to-see-new-messages-in-a-thread).