@Eric Watson Your workflow looks good and I have tested the same at my end but couldn't observe any issue. Can you share more details on how you are getting the content using one drive connector?
As you have already confirmed that the same pdf opens correctly from the SharePoint site. I believe your workflow get the content from one drive and upload the pdf to the SharePoint and send an email with the attachment. Did you observe the same behaviour for all the attached files or only for the few files?