I would assume that you are using a B2B Listening channel to pick messages from a folder. Please check if this Listening channel is having the Enable Marker parameter selected.
Disabling the Enable marker should avoid generation of the .mark file in the folder.
Thank you, Arun. That works. Somebody enabled "Enable Marker" parameter not of our awareness. We unchecked it, and everything works fine as before.
Thank you again for your response.