That sounds incredibly frustrating! It’s definitely a weird issue, especially since you’re already partway through the quest. Since you're running mods and Debug mode, it’s possible there’s a conflict or a script triggered incorrectly.
Have you tried checking your quest log to see if it updated properly after catching them? Also, have you tried sleeping in-game or warping to a different area to see if he respawns? Let me know, I'm curious if we can figure this out!