So, I adopted a Zentu at 1:38 AM because I wanted the night version, but I have somehow ended up with a day version. Is this a bug I can report or is there something I don't know about the times?

You have to go when it's nighttime in Shengui Guo, which according to this thread is 3pm to 1am Subeta time. Unfortunately you just missed it :c

Drat! Thanks, Do you know if there's a way to change it to a night version yet?

You can use which is in Five Seven Five for 250k sP c:

Thank you so much!

You're welcome! I forgot where the elixirs were stocked until I went to look it up, I'm glad it's not too expensive ^_^