Hello, I have played several games where I faced the exact same problem : no matter whether I am playing a custom faction or the AI opponent is playing a custom faction, as long as a custom faction is defending a planet, when they draft, they do not lose pop. I do not believe it's simply a coincidence linked to pop growing at the same time that they lost one, since it has happened many many times.
I play exclusively on Endless speed, so maybe it's linked to that. The bug has appeared for multiple different custom factions I created, with various traits.

draftbug.sav

Here is a file save from one of my games. (Sometimes the AI is stupid enough to protect the system instead of drafting, I guess reload until they make the right choice). Initial pop on the system attacked is 9, then you choose to resolve the fight, they draft, the combat shows population lost 1 and draft, but the pop of the system is still at 9.

Can you provide a diagnostic (Documents/Endless Space 2/Temporary Files) of when this is happening

Uh it keeps telling me "something went wrong. Try again" when I upload file. Can I send it to you by mail or something it's Diagnostics - 2024'01'11 @0859'22'' takes up 2051 Ko

Does this work?

https://drive.google.com/file/d/12QGEEX30bbbf8SiOiP70f4AxlUrGMKts/view?usp=sharing

You need to change the sharing settings so that anyone with the link can view it.

Sorry, I didnt check in a while. Is it good now?

Yup, though I looked through it pretty thoroughly and didn't see any errors so it's probably unintended behavior rather than a bug.