With the last version of Ghost, the footnotes are being generated by each section of markdown, and not by the entire post.
For example, if you have a markdown section with a footnote reference, next, you have plain text (outside of a markdown section), and in the bottom, you have another markdown section with the footnote definition it'll not work.
However if the reference and the definition are in the same markdown section it works, but the definition will be rendered in the bottom of that markdown section like this:

As far as I understood, this is happening because these two markdown sections are not being compiled together, so the parser doesn't detect the reference nor the definition of the footnote

@albizures this is expected behaviour. General footnote support is not present in Ghost 2.0, if you need footnotes to work across the entire post then you would need to handle them manually by adding your own superscript links and adding a HTML footer or by using a single markdown card.
As an example for manual footnotes, you can type ^[1]^ to create superscript formatted text like [1] then you can select it and apply a link, eg. "#my-footnote". Then at the bottom of your document you can have a HTML card containing the named links and formatted in any way you want.

If you want to vote on more integrated footnote support then there is a feature request open on the forum https://forum.ghost.org/t/footnote-support-in-editor/1521
thanks, @kevinansfield for the quick response and the workaround
Which version brings in the built-in footnote support? I am using 3.0.3 and cannot get it to work.