It’s strange that it’s only for some utterances, I would expect the NLU, etc, to have consistent processing times.
If it’s only happening for certain users, it could be the tracker store. Most tracker stores store and retrieve the entire history to process any message. The reason we chose the SQL tracker store is that it only retrieves history for the current session. Dialogue tracker gets too big
If it’s happening for certain actions, especially for custom actions, then I would look what those are doing, and maybe benchmark and profile those actions to see where you can make improvements.