The sheet causing issues is likely an odd size. Our system is optimized for 8.5x11 and when it sees a different size it doesn't know what to do. That is why it is being rotated.
If you have a document that won't fit properly, you most likely need to Print it to PDF, which will resize the sheet to 8.5x11 inches. You can clean/re-size any PDF for upload to our system by following these steps: https://submittal123.groovehq.com/knowledge_base/topics/print-to-pdf
Contact our support team for further questions.
Regards!