Some spell gems, such as “Dark Ritual”, are clearly intended to be used only on your allied creatures since they instantly kill the creature. However, the description only states “target creature”.
In other cases, such as with spell gem “Anger”, which sets “target creature’s” attack to be equal to its intelligence, one might expect this to be usable on enemies too. Perhaps it’s supposed to be and is a bug, I am not sure - but I was only able to target allies with it. I chose the creature (Arena draft) partly because the spell gem looked useful for cutting down the attack of “brawny, but dumb” opponents.
My suggestion is each spell gem which affects only enemies or allies should state such. Most of them do already, so it’s probably just a small handful that have slipped through.