Take a sentence like "Isn't that it?"...

"Isn't" is a contraction of "Is not", right?

So why do we expand it to "Is that not it?", the not has moved position, shouldn't it be "Is not that it?", yet saying things that way either feels old fashioned or wrong.

Either the contraction should expand in the correct order, or we should change the contraction, i.e:

a) "Isn't that it?" = "Is not that it?"
or
b) "Is thatn't it?" = "Is that not it?"

English is illogical. :(