When constructing the Eternal Flame, production stops, but is not lost, when your Fire Mana supply is interupted. I'm not sure if that is intended or not.
Religions will spread to cities that already have a religion. Also, you cannot spread the Order to cities that have the Ashen Veil and vice versa using Acolyte or Savant units. However, you can convert to one of the religions and use the priest to spread the religion (and build a temple). Again, not sure if this is intended or not since documentation is...lacking

.
When you construct Genesis, it turns Ancient Forest on grassland tiles into regular forests again. I only mention this because my city of 26 suddenly became a city of 22 =/.
The tax and research settings are very buggy. They will randomly decide to auto-correct themselves, which often includes a change in the specialists assigned in your cities. I'm not sure what triggers this, but roughly 50% of the time it happens after a large change in gold production (A new religious capitol building, bazaar of mammon built in a religious capital, etc.).
I am also unable to add or remove Engineer specialists in a city.
I think the Halls of Granite is
way overpowered. Reduce the bonus to +25%, at the most, for having stone.
The following buildings are set at +/-1% trade ruote yeild. I assume this is meant to be +/-1 trade routes or +/-10% trade route yeild.
Overseer's Residence
Shadowed Veil
Theater of Dreams
Golden Wood
You might want to make Treants national units.
All of these issues were encountered playing as Perpentach. I was using a large Tetonics map set at 70% water, temperate, noble and epic. I'm gonna try out one of the good civs on the next play through.
EDIT: Oh snap, I almost forgot. Perpentach is not able to construct Obelisks. You always forget the first things you notice v_v.