Hear this...
They time traveled six months before the actual Annihilation episode. So, when the Turtles stop the Triceratons, won't they interfere with the Turtles that were on Earth during those six months?
When they defeat the Triceratons, the Earth will remain intact, but you'll have two types of Turtles along with April and Casey. The ones that are exploring the Universe in Season 4 AND the ones that are on Earth during the said exploration!
This has been bugging me for a while...