Reimu says that her concern about the potion possibly being the cause of an incident was correct, and that what is happening to us now is indeed an incident. To say that the potion is unrelated to what's happening now contradicts that. Therefore, the じゃない here is probably not intended as a negation, but as a way to emphasize or assert an opinion.
...Aaaagh.
I knew it'd be the source of an incident.
Eh?
That we've become like this is an incident.
It's certainly an incident.
...That's right...
And incidents need to be resolved.
*breeze*
Because, what's happening now isn't because of that potion.
