It may be caused by OneNote file failed to sync with SharePoint. You could refer this article to troubleshooting the issue.
- In OneNote, click File -> Info -> View Sync Status.
- In the Shared Notebook Synchronization dialog box, click any notebook icon with a yellow triangle warning over it to see the name of any section that’s causing sync problems.
- Click the Sync Now button next to the notebook containing the section.
- After the section syncs successfully, then download file from SharePoint, open again, compare the result.