After looking into this some more I found that pdf files seem to assume/ require fairly large margins. While most printers can print up to arround 0.5 cm margin pdf readers assume a minimal margin of around 1.5 cm.
For the tex document I can either adjust the margins so that the pdf readers are satisfied or ignore the warning and then print with or without shrinking.
Edit: Clarification for the comment below. The shrinking/ margin issues only appear when you try to print the document. As long as you look at it on your screen, it will display fine, even if the document goes all the way to the paper margins. Take a pdf document that only has 0.5cm margins, try to print it and the print options will try to either shrink or believe the printer will cut off the margins.
Here is a small example:
Edit2: After some browsing on stack exchange I found these two related questions:Prevent scaling of printout of PDF without using hyperref and PDFs want to scale down. This seems to be a known issue of the pdf format and the acrobat reader and there are tex ways around it.