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This happens kinda often, especially in stuff that doesn't explicitly have a prologue designated.
To use the example that inspired this thread, take the webcomic Ava's Demon. Now, the way I see it, there are two possible places where the prologue could be considered finished: The end of chapter 1, or the end of chapter 2. The issue with classing chapter 1 as the prologue, however, is that not a whole lot actually happens. To be precise:
* We find out Ava is possessed by a demon.
* We find out that the comic is set in 3031.
* Ava gets expelled (and we also learn that she used to be friends with Maggie).
* The planet explodes due to the Silent Scavengers.
Compare this to chapter 2, where several events that are clearly significant to the plot at large. Namely:
* Maggie is very strongly implied to have made a pact. (Although that isn't really clear until we find out the effects of a pact in the later chapters, so.)
* The ship crashes on a new planet and Ava dies.
* Wrathia's identity and past is discussed, along with Ava's by extension.
* Ava makes a pact and stops being dead.
Now, the way I see it, Chapter 2 is far more significant to setting the scene than Chapter 1, making Chapter 1 + 2 serve far better as a prologue than chapter 1 alone.
In a similar vein, Dragon Quest VII. Does the prologue end an hour or so in once you hit the first island, or at the end of Disc 1, when you release the main villain and the plot actually starts properly?
I guess it's not really important in the grand scheme of things anyway, but still.