While having a chatbot is helpful in catering inquiries from potential leads or customers, unnecessary replies may leave a bad impression, especially when an agent has already taken over.
Chatbots will only stop sending automated messages after replying via HubSpot.
When responding to messenger conversations, make sure that you are using your HubSpot account. Else, the chatbot will continue to send automated messages as well as remain in the bot flow since it does not recognize agent replies coming from Facebook Messenger.
The thread will only be assigned to an agent and removed from the "Bot" folder, when the agent replies using the HubSpot interface, and not Facebook Messenger Interface. If the reply is from Facebook Messenger, the system will not recognize that the message should be assigned and will still be inside the bot flow until the Contact/lead reaches the action to be routed to a team member.
At the moment there are no options/settings that would allow you to transfer the replying functionality from HubSpot to Facebook and be able to have the same result with routing.