So you want an explanation for how magic works or?
Since I don't see it being any different from any other fantasy wherein people play with magic and accidently creates something bad. Saying that non-omnipotent magic can't create omnipotent magic is rather silly, since it is magic you know.
Magic still should have rules and a bit of common sense.
It's not silly.
It's not different that a 9mm bullet doing more damage than a 120mm cannon shell.
It's called consistency. World building.
Not creating a thousand plot holes and open questions.
If mages that can't even do First Magic can create a Grail, then what's the point of the Grail or the Grail Wars?
Why didn't older mages, who were more powerful, simply made a spell to make the entire world theirs?
Because magic.
Archer shoots arrows from his butt. Because magic.
Rin wins the war by not fighting and getting killed. Because magic.
I'm in a hurry, and the shortest way to my destination is a straight line. But I will go in a circle. Because magic.
I'm a genius writer, the above plot is perfect, because it's magic.