Can you try reloading the game (maybe through an autosave near the end?) and defeating them again? Does that bring up the achievement?

I actually has something similar happen, but with the relics. There's an  achievement granted when you control all the relics. I thought I had it in the bag since I had built or bought out all the starbases that were linked to relics and made sure I upgraded them to have xeno-archaeology. Even after the game ended I didn't get the achievement. It worked in a new game that I started later though.

Just had this happen to me using version 1.61. I conquered the Iconians' last planet using cultural takeover (i.e. they defected to me).

Two days ago, I won a diplomatic victory as the Snathi.  Since the Snathi are not well liked by everyone, I thought this was a notable achievement.  Steam did not think so, nor did Metaverse.  My reward was only four points!!??   I have no credit on Steam for winning as the Snathi, even though Metaverse confirms the win.

I can't send a saved file.  I always play using only one save and am now ten hours into a new game which over-wrote the Snathi file. The Snathi game was played on 1.61.

I love the GCIII.  I have almost 500 hours of happiness and frustration.  Great value for the money spent...but I HATE the scoring system.  It is NEVER explained.  I am no dummy at GC III and am in the top 50 scores on GCIII's Metaverse.  I was number 9 on Gal Civ I.

I re-loaded the save game from before I won, and I conquered the last planet by invasion instead of cultural annexation. This time I got the achievement. Go figure.