Ouch, yeah. That's fucked up. The middle energy refresh package, (what, 175 gems?) would have almost certainly enough to get 14 arrows. (possible with lowest) Just did an experiment, (checked what it would take me to craft Asuka after having bought everything else I was interested in:147010 gems. So it's not like there was a bug where it didn't give you credit for the mats you already have. I think it's a cool idea being able to buy whatever is missing, (never even occurred to me to try, to be honest, I don't think I've seen that in any other game. You miss it you miss it) but the price needs to be *much* more reasonable. At that point it may as well not even exist.
(I assume you're stuck with an iPhone? Guess stuff like this is another reason to go android. Though, to point out, you presumably knew you were just short before you left, and could have bought some extra energy to make it then.)
So, yeah. The ability to buy what you missed is a cool feature, (and I'll have to remember it in the future, instead of just blowing all my mats on whatever when I realize I can't get enough for anything more I really want) but either they're F'in retarded or they slipped a decimal point. 350 or so would have made some sense, 2x what it would have cost you if you had done it when you could as way of penalty.
That said, there *is* a screwup that's 100% in the players favor (that I'm not going to mention in case other people know about it. I'd assume the devs monitor these threads, and will fix it if I do. I figure the screwup on the decimal balances out this screwup, though unfortunately it won't help you get more arrows.)