This is in reference to my question on tex.SE here.

When converting from markdown to beamer, the citeproc adds the specification overlay of <.-> to the foonote command when using footnote citations.

If I use the `. . .` in markdown to insert a pause, this footnote will now come one slide early. This is because the "." in the <.-> takes the thebeamerpauses and subtracts one. 

See section 9.6.2 of the beamer manual, as well as this helpful article.

I know that if I use the ::: incremental div block, that it converts to beamer in a way that this specification overlay will work (because this uses the <+-> overlay, which increments beamerpausus after the command)

However, the problem with the ::: incremental div block is that it ignores sections. So if I put a section header inside my frame in the incremental div block, it still shows up on the first slide. If I use the pause command, the header will not sure up until after the pause, which is what I want. 

Seems like there are two different things that pandoc does, and the footcite only works for one of them. Maybe would be helpful to be able to somehow send an overlay offset to the citation command or something?