Translation:You cannot pay yet.
"Can not", "cannot", and "can't" are all the same. M-W simply defines "cannot" as "can not" (https://www.merriam-webster.com/dictionary/cannot), and the same goes for "can't" (https://www.merriam-webster.com/dictionary/can't). The OED says "cannot" is preferred over "can not", unless the "not" part is part of another construction (https://en.oxforddictionaries.com/usage/cannot-or-can-not).
For example, "a pedant can not only be annoying, but also be wrong."
In American usage, if I say "you can not pay", I mean that it's okay for you to not pay. When you break up the word like that, the not is actually part of "not pay" rather than "can not". That's what Ichigotchi was referring to.
I think you may be taking past each other.
Phillip did not ask about cannot versus can not. I agree that the placement of "yet" in the English doesn't change the meaning.
But I also agree with Ichigotchi that "cannot" and "can not" mean different things. I think the Japanese means "cannot." But Duolingo is correcting me with "You can not pay yet," which seems technically wrong. It should be "cannot."
(This is probably not why it corrected me: I said "I" not "you.")
I think this particular sentense is situation specific. In Japan, there isn't a custom to leave money on the counter or table to pay. Monetary transaction happens either when purchase is made(fast-food places, for instance) or in the end, after eating/drinking and one is leaving. Also important to note, we do not leave tip on the table, it isn't a tipping culture. As a native Japanese, this sentence makes me think of a situation where I am with someone who is foreign to the practice and taking money out to leave on the table and I am telling him/her not to.