Harnessing Lightning
I would ask the players what happened.
Player A could say many things:
“I cast Harnessed Lightning to deal 3 damage, but Spirit made it not die”
“I cast Harnessed Lightning, gained 3 energy, then didn't use any since it
was Indestructible….oh, I should have 3 energy marked”
“I cast Harnessed Lightning, but he made it Indestructible for the spell
fizzled.”
etc
The player may have assumed that he had to spend 3 energy no matter what.
If so, the game state is fine. He may have not use any energy, but forgot
to visually mark it. He may have thought he never got the energy because
of the Selfless Spirit. All of these situations look the same. However,
we shouldn't always just look at what physically happened and assume the
set of actions that led to that game state. Take a second and ask players
what they believe happened. You'll often find that what appears to have
happened is not what the player(s) believed happened.