You can also find and parent orphan pages by going to the Reorder Pages function in Space Tools. Simply drag each orphan to its new place in the hierarchy. Orphans appear as top-level pages along with the space's home page.
By default, new pages are parented to the page users were on when they choose Create. The most common case where I've seen people create unparented pages is when they don't go to a space where they can add a page before choosing Create – if users typically choose Create from the Dashboard, for example, and then choose the target space in the resulting dialog, then they can easily create orphans. I don't know a way out of that, other than user education and rescuing orphans by hand. Ideally, users are trained to go to the page that should contain their information before choosing Create.
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