I'm also experiencing this problem after updating from 1.15.2 to 1.16.1.
Using the same seed on a fresh 1.16.1 map and the same portal location, I could not reproduce this in a local or server game.
I have also seen one location where the player was randomly dropped between one of two phantom portal locations. The two locations did not change, but which one we are sent to does.
One user on IRC also experiencing this issue suggested there may be "something hinky happens with the nbt at some point."
I first saw this in a map running spigot. I moved over to a vanilla server, checked all portals, and found the error in one of those portals.
... It's rather appalling that you just defaulted to marking this Invalid/Resolved without gathering any details. This seems to be a common trend for issues you're involved in. :/