What is the issue?
The PDF does not comply with the PDF specification according to ISO 32000.
What does it mean?
The message "MCID <x> already present." means that there is a "Marked Content" (MC) that has already received an existing ID (and the ID is therefore used multiple times). Multiple MCIDs are not permitted according to the PDF specification and render the PDF invalid.
In the tag structure, marked content containers are addressed via MCIDs in the content streams. The MCIDs must be unique within a content stream. If there are several marked content containers with the same MCID in a content stream, this represents an ambiguity that may not be able to be processed by assistive technologies.
How to fix it?
This issue can't be fixed with axesPDF. You could try to create the PDF newly.