Now that I'm thinking more about the issue, the planet was fine for most the game then the Yor population went down. So the problem is probably tied to a precursor world tech. Hope that helps find the bug!

It happen to me too, i use Synthetic YOR the Population Drop From More than 20 to 1 pop in the planet

Its happen in my capital too, luckily i have several planet in development progress, here is my suspect of the bug :

1st planet (Science Precursor) have its housing upgraded to level 5 , The population will go down from any number to 1 in the planet, even if i manufactured the citizen, the next turn it will reduced by 1

2nd planet (Capital, normal) have its housing upgraded to level 5 , The population will go down from any number to 1 in the planet, even if i manufactured the citizen, the next turn it will reduced by 1

3rd planet  (Production Precursor) have its housing not upgraded (Lvl 0), The manufactured citizen stay after the next turn, and allowed to grow until it capped

4th planet (normal Planet ) have its housing not upgraded too, citizen can grow till capped

So yeah,  i think its because i upgraded the housing level