The problem is that you are putting LaTeX between a rock and a very hard place.
A very rough overview of how LaTeX type set documents
LaTeX doesn't just put line after line after line. It tries to also maintain certain aesthetics about how the page should look. Some things it tries to avoid by default
- Ending a page with a section heading
- Ending a page with the first line of a paragraph
- Beginning a page with the last line of a paragraph
- In a book (two-sided) document format having the top and bottom of opposing pages at different heights
- Having too much vertical space between lines/paragraphs
Usually the typesetting engine tries its best to adjust the whitespace between lines/paragraphs, moving some lines from one page to another, and do other sorts of adjustments so that all of the above (and other things) can be avoided at the same time. But sometimes it is just not possible (because the text you give it just happens to be the "wrong length"). When this happens, it will violate one rule in other to make other rules happier. Which rule to violate depends on the penalties you assign to them (and there are some defaults built into the various document classes).
What likely is happening
You probably have the section title set in relatively large font. And chances are, if you read the compile log provided by LaTeX, you will see that you have an
underfull vbox warning. (See also this question.)
Before inserting the footnote, the text probably looks something like this:
After inserting your footnote (which takes up some space), some of the text on page n gets pushed to page n+1, so that LaTeX is facing the choice between the bottom of Page n+1 looking like
which its aesthetics tell it not to do, or moving the section title to the next page. But if it makes the section title to the next page, the space that it would otherwise have occupied on Page n+1 is now blank. And leaving it like that would violate the rule about having the bottom of the pages lining up.
So to compensate, every paragraph on page n+1 is shifted somewhat. If you only have two paragraph breaks on page n+1, and the space that used to be occupied by the section title and the first line of the next paragraph adds to to be about three lines in height, you will see a gap between paragraphs with height about 1.5 lines being inserted.
(The details of the above description may not be 100% correct, or 100% describing your situation. Short of seeing your code we cannot say what is the exact reason. But the general idea should illustrate to you what is happening.)
What do you do?
It is apparent to me that you are still in the middle of composing the document. And because your content is still mutable, this is not the time to be worrying about whitespace issues. (For that matter, this is not the time to be worrying about fine tuning any formatting issues. If you "fix" it now you will likely run into another problem later.)
When you are finally done with writing your manuscript, and is ready to print it, then it is time to worry. And what you can do is either change the penalties or change the stretchiness of paragraphs or rewrite the text (increasing/decreasing the lengths of individual paragraphs, move the location of figures, moving equations inline or into display) so that the "problematic behavior" no longer appears. If you are not very comfortably familiar with what TeX does to typeset your text, you are most likely better off doing the last of the options above.
This Q+A item may also be helpful.
\raggedbottomin your preamble. that will make the bottoms of the pages uneven instead.
twoside) and LaTeX tries to finish all pages at the same line on the bottom. Try