Just figured out my error. Had nothing to do with file size. Both of the XML docs I had that were over 5mb had parenthesis in their file names. When I would delete some table data out of file contents making them below 5 mb I would save them as "test.xml" taking away the error.
When I was running in Dev mode there was no issues in the Windows OS, but in Ubuntu, if the file with parenthesis in the name was uploaded, it would wrap the new file name in apostrophes to save it in storage.
I just used str_replace to replace parenthesis with underscores when saving in storage and saved the original file name in the db.