Hi there Casto93,
From what we can tell, when attempting to use Markup with your Apple Pencil on PDF files in Safari on your iPad, you're seeing a completely black document instead of the actual written content in the PDF. We're glad you've joined us in Apple Support Communities, and we can provide some guidance.
To start, you'll want to be sure you're saving the PDF to the Books app to edit it from there. Not all websites in Safari allow you to edit content live, directly from a browser like Safari, and that could be related to why you're seeing a black screen.
"You can save a PDF from your email or a website into the Books app. You can also save a webpage or email as a PDF, import PDFs from other apps, or use your Mac to add PDFs to your Apple Books Library." Have a look at this support article to learn how:
Save and mark up PDFs on your iPhone, iPad, or iPod touch with the Books app
Also, you may find the links below helpful when using Markup with your Apple Pencil in the future:
Use Apple Pencil with your iPad
Use Markup on your iPhone, iPad, or iPod touch
Cheers.