It is likely that your shop logo is too large. Could you please try converting your logo to JPEG, if it is in PNG, and resize it to a max width of 400px?
Please note that we store the plugin’s settings in the order, within the invoice data, therefore, enable the Test mode option, under WooCommerce > PDF Invoices > General, if you want to test the new logo in a previous PDF document.
In addition, try activating the Enable font subsetting option as well, that you will see below the Test mode, to reduce even more the size of the PDF documents.
This is an example of a perfect shop logo for the PDF documents:
When you have managed to reduce the PDF document, please do not forget to disable the Test mode again!