Today, I tried to use “Magic Battle-Training Stone” on Snoots. I clicked on the stone and then clicked on Snoots’ profile in the journal. I received the error of “Invalid Target”.
However, when I summoned Snoots and then used the stone, it worked. This is odd because previously, I could just click on the pet portrait in the journal and it worked fine. I’m hoping this is a bug because it’s an extra step that seems unnecessary.
Has anyone else experienced this?
At one time I seem to remember Blizzard mentioning could just click on the Journal but it never worked for me. Don’t know if it got tried and later abandoned.
Maybe it was just a glitch for me earlier. Because just now, I tried using a Flawless Battle-Training Stone by clicking on the pet portrait in the journal and it worked fine.
The differences are that it was a different type of stone, a different pet (Extinguished Eye), and I am in a different zone (Hallowfall instead of Dornogal).
Why I really like this forum. My keystrokes-per-day count will probably drop 30% now that I find out just clicking on portrait does indeed work now and I don’t need to do a summons anymore. Thanks !
Was in Valdrakken, used Fel-Touched and Flawless Battle-training Stones. Will watch to see if stone type or location seems to make a difference.
I remember someone had a similar problem, but instead the battle-stones were consumed in excess.
Turned out, even if you pick a pet in the journal, whatever NPC you’re targetting outside is getting prioritised.
Because the OP was targetting a non-rare pet directly, and the quality used not to reflect ingame until resummoned, they wasted a handful before figuring it out.
In your case it might be you were targetting someone or something else entirely. 
What doesn’t work, left clicking on stone, then on name in Pet list or queue.
What may work, clicking on pet’s icon in journal, then on stone. (may need right click not left).
What DOES work, summon pet, Highlight them by clicking on them, then RIGHT click on stone.
Understand that we’re talking here about having the stones in your bag, not in bank. If a stone you need is in your personal bank, guild bank, or WarBank, you have to move it to your bags to be able to use it on a pet.
Right-clicking on the stone, then left clicking on the pet in your pet journal will apply it. Or summoning pet and either left or right clicking on it to select it, then right-clicking on stone in your bag.