Sometimes it is easier and faster to layout small books as the one story. But in some cases when the new chapter stars on next (or next odd page) footnotes shold be at the end of the text on previous page.
One simple option can resolve such problem.
Please add the new option to the Document Footnote Option > Layout > Placement Options:
"Place the footnote at the bottom of the text when on next page the first paragraph has the attribute 'Starts on next Page'"