Best answer
Most often the flow was not waiting for a reply in the first place. A flow only resumes on an incoming message if it reached a step that parks the run and waits; otherwise the run already finished and their reply is just a new inbound message that no longer matches any trigger.
So there are two separate questions, and they have different fixes.
Did the flow reach a waiting step? Steps that ask a question and wait, or that collect an answer, park the run. Steps that only send do not. If your flow sends three messages and ends, the run is complete before they type anything.
Did the reply match what the step expected? A step waiting for a specific quick reply may not accept free text, and a collect step may reject an answer that fails validation.
Check the run in the automation's history. A run sitting in a waiting state means the flow is holding for a reply and something about the incoming message did not satisfy it. A run marked complete means the flow ended and you need a trigger for the follow-up message, not a waiting step.
One more cause worth ruling out: if a teammate replied by hand in the Inbox first, the conversation is no longer automated and the flow stops on purpose.