Whenever you implement the integration between Dynamics 365 online and SharePoint online and when you hit 5000 or more documents per entity we might experience resource throttling.
This resource throttling can affect other features. For example, Microsoft OneNote integration will not work when the SharePoint Server site has 5000 or more documents.
Anyway that is not so true and we can bypass this:

Repro Steps:

1) Open Dynamics and navigate to the entity that is enabled for OneNote integration;
2) if this entity has library with more then 5000 documents uploaded, clicking on the "OneNote" button will not open automatically the document and at the first check looks like that the button do not work;
3) if we click on the "Document" option button, we are going to see the Document Management Page and all the documents that are uploaded for this entity. We can see there and the OneNote document which we created on step 2.

The system behavior could be change to the bellow described it:

1) Open Dynamics and navigate to the entity that is enabled for OneNote integration;
2) clicking on "OneNote" option button to open the Document management page which is equal to what the button "Document" option do;
3) the OneNote document will be visible there, still it is not going to open automatically, but at least we can open it from there and we are not going to get the error message when we click on the "OneNote" option.