A couple times in 2 different games has several systems I own lost population every turn. Once I thought it was because of mass terraforming, but the second time was much earlier in the game when I didn't terraform anything.

The planets were happy, not under siege, and I was not making any colony ships. It could happen every single turn back-to-back. It could happen to several systems at once, eventually crippling them completely. There was never an in-game message that explained any of this.

I noticed that the timer for pop-increase was always at 1 turn for every system it happened in. Could it be some weird factor where if I overproduce food it somehow ends up as a negative "growth"?

Sadly I don't have the specific save file anymore, so I can't share it. But saving and reloading seemed to fix it, so might not be related to mass-production of food.