(update) see this thread: https://www.games2gether.com/endless-space-2/forums/114-bug-reports/threads/27006-vodyani-missing-pop-ark-consumption?page=1

• Summary / Title: Can't build more than 2 vodyani pops
• Description:  Tested on 4 different new games with 1 or 2 ark attached systems. Even if the the third pop placement is free and unlocked, building a third pop just push the popmeter to plain 2 and tendance to negative (loosing pop). Spending 500 essence or even 1000 (2 more tries) won't create this third pop.
• Steps to Reproduce:  1. make a new game 2. when you have enough essence build a third pop on an ark attached system
• Reproducibility: 5/5
• Expected Behavior: Ark attached systems should gain a third pop.
• Version: 1.0.11 and 1.0.16
• Notes
• Attachments: 2PopCap.zip

not confirmed. i was able to build the 3rd one just fine 6 out of 6 times on 1.0.16 

however if you have negative food income you can lose the pop immediately.

try increasing your food prod (to positive) and make a pop.

edit: false report loaded up the save and your -4 food is the cause. however loosing a pop due to lack of food is kinda weird but not a bug in the traditional sense. i would call it a design flaw

Seems to be the same issue, well spotted.

edit: just confirmed with a new game.