Thanks. I think you've definitely uncovered a major bug here. The way copy and move works has changed drastically for Sonoma and it looks like there is some case here my testing hasn't caught.
I can replicate this for a Copy Files action when copying a folder but it works as expected for Move Files actions. Is this what you're seeing?
Also, if you try one that doesn't work and then open the grid and press the key combo Cmd+Shift+D (to open the debug console) can you paste the output.
I'm investigating this as top priority so there will likely be an update out to solve it very soon.