Things that I have seen : ( wife was a production editor, I briefly helped an EIC of a society journal that was sold to a publisher )
1. Graphs do not fit the page or space allotment - journal is uses two column format, author decided it did not apply to them. Graphs do not fit the color scheme - the author decided that the graph will be blue and the legend would be green. This is a black and white journal. Graph is a photograph of a graph, not a graph. Photo was taken on an iphone.
2. Sections went out of order. Author did not use the numbering system and numbered them by hand. Author cross referenced sections by hand, changed the ordering and did not update all of them, referring to non-existent sections.
3. Footnotes referred to non-existent papers.
4. Author included someone else's figures. Author did not obtain a permission to use them.
5. Accepted paper is written in a monospace font in WordPerfect for DOS. In 2014.