The difference is that when Tails and Sonic are seeing themselves in the sky, they see reflections of them together the way they would like to be. When Sonic sees Tails in the sky, Tails is nowhere to be seen, and Sonic is all alone while sad music plays. It's a conclusion made through the identifying factors during the ending and comparing the two together.
Even so, if he's alive and kicking with his constellation in the Good Ending, couldn't he be alive in the Bad Ending as well? Maybe he's just working for Robotnik now.
I guess it might be a case of Came Back Wrong or something? Like Sonic saved Tails, but Tails isn't the same, or the Tails he knew was changed somehow.
Sonic the Hedgehog 2 has the Oil Ocean zone. Dr. Robotnik's boss machine in that level spends its time submerged in oil. When you defeat it, it explodes. Why does this not affect the oil the machine has been covered in the entire time? Or the entire ocean of it making up the level, for that matter?
Not to mention another highly-known attribute of oil: being covered in it is of great harm to animals. Sonic doesn't even have to brush it off.
It probably just flies off when he runs at supersonic speeds.
In Sonic 2, what happens to all of those animals that fall from the sky in the Sky Chase zone?
Well, there's no falling damage in this game...
Small animals don't usually fall at terminal velocity. Cats and turtles, for example, can fall out of planes and land (relatively) unharmed on the ground.