Hi Jakub,
Thanks for posting in the community. We are happy to help you.
According to your description, I have tested it on my side, and all embedded files can be pasted successfully. Please try to repair the OneNote application, and then check again. Since there are two OneNote applications for Windows, you can choose the related steps to repair your OneNote application.
Repair OneNote for Windows 10:
Quit OneNote for Windows 10, go to Windows Settings> Apps> Apps & features> find and select OneNote for Windows 10> Advanced options> Repair. After that, please run OneNote for Windows 10 and check again.
Repair OneNote (previously called OneNote 2016):
Quit OneNote for Windows 10, go to Windows Settings> Apps> Apps & features> find and select the Office suite (the Office suite contains OneNote), such as Microsoft 365 for Business, then select Modify, Repair, Online Repair. After that, please run OneNote and check again.
If you have repaired your OneNote application, but the problem still happens, I would like to collect more information to troubleshoot.
- I wonder which OneNote application you use.
- Does the problem happen in a specific notebook or all notebooks? You can create a new notebook to test.
- What if you use another OneNote application, does the problem occur?
- Please provide your OneNote version.
OneNote: click File> Account, please take a full screenshot of the current interface. You can click "Insert Image" to upload it.

We look forward to your response. Thanks for your cooperation.
Sincerely,
George | Microsoft Community Moderator