Which has no effect on the wikitext you get back to save, because you didn't edit the transclusion itself.
I just ran into this myself: https://meta.wikimedia.org/w/index.php?title=IRC/Channels&diff=12412456&oldid=12002898
In this case I copied the {{Channel}} from the wikimedia-design entry, and it copied correctly as a template, but I could still edit the contents directly (as I could before copying), and thus the transclusion itself remained the same.
Might be caused by Parsoid?