I was having the same issue! but I figured it out, you have to add a "wait to return" to make sure the pythonista code finishes running before the shortcut does. Hopefully it was the same issue if you haven't figured It out yet.
This is the community forum for my apps Pythonista and Editorial.
For individual support questions, you can also send an email. If you have a very short question or just want to say hello — I'm @olemoritz on Twitter.