Thank you for your post. Can you please contact our Support Team at firstname.lastname@example.org? They will be able to assist you to investigate what is happening. From your description it sounds like there is a bug, it should should pause the entire tracking process, but our Support Team will need to ask additional questions that will be better handled over email than a forum.
Adobe released an update to Illustrator 2021 (v25.3) that includes native support for M1 Devices and Rotate Artboard functionality. Please note these features are not yet supported within MAPublisher at this time. See compatibility notes.