So I came across a temporary solution, removing the 'content-length' setting out of the page headers fixes the issue.
The explanation of 'the site breaking' is that the content-length bytes sent in the header of the a webpage did not match the actual size in bytes as the page that was sent from the server. This was caused because the content-length header was being set before the pagespeed module was applying it's changes to the page. Therefore, it caused the actual size of the page to be larger than what the headers said, and that caused browsers to cut off the page at the length specified by the headers.
The pagespeed analyzer also did not like this, because of the discrepancy it said that the pages could not be viewed by a browser and so it could not get a score for them.
I cannot send a url because it is in a testing environment, but I have tested with ?ModPagespeed=off, and when doing that, the content-length mismatch is no longer an issue.
Thank you for your responses, any information on setting the content-length after the pagespeed mod runs would be helpful, currently I am just not putting them in the header, which is not ideal for production.