Since this story generated so much unexpected amusement on the internet, I decided to share it here as well.
For the 3 figures in the manuscript, we created some adjacency matrices that we wanted to be fully reproducible, so we decided to upload our code.
Because I had anticipated problems with .R files, I uploaded the syntax as a .txt file instead. A month or two later, when the manuscript appeared online, I found out that the copy editor had first taken screenshots of each page of code, and then put these screenshots into a word file that was available as supplementary material to our paper. You can find this piece of beauty for download here.
See below for the somewhat flabbergasted email I sent to the editor: