A few months ago, we published a new paper1 (PDF).

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:

Footnotes
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Fried, E. I., van Borkulo, C. D., Cramer, A. O. J., Boschloo, L., Schoevers, R. A., & Borsboom, D. (2017). Mental disorders as networks of problems: a review of recent insights. Social Psychiatry and Psychiatric Epidemiology, 52(1), 1–10. ↩