This is another long-standing area of weakness for FM. The footnotes behaviour is not well-controlled when there are many per page, as you are seeing. It's sometimes less frustrating to convert the footnotes to endnotes (i.e. make cross-references instead of using FM's built-in Footnote tool). Alternatively, creative editing and copy-fitting are needed to lessen the number and/or length of individual footnotes falling on any one page.
Another, but more risky (i.e. maintenance issues when updating the documents) is to do the footnotes manually using cross-refs and a manually-sized secondary text frame at the bottom of the respective pages. This creates a substantial number of page overrides, but it may give you the control that you need. If the documentation is frequently updated, then I wouldn't readily recommend this approach.