Uploading Illustrator file issues

I recently had an issue with uploading Illustrator files to an online contract printer.  The issue is elements that were deleted prior to saving (not simply hidden) are showing up in the file once uploaded.  Or on one, I re-sized an image from 11.5" to 9".  Once uploaded, the file showed two images on top of one another, a large file and a smaller file of the same image.  Is this a strange bug with the history tool?  The only work around has been to place the final image on a new canvas and then save as a new file.  Never had this happen before and I've used this contractor for quite a while now.  These files all were saved in the last week.