It appears that one is not supposed to use \footnote in math mode as per this appropriately named question: Footnote in math mode. However, it appears that I can get it to work without having to resort to \footnotemark and \footnotetext, as long as I use a minipage:
\begin{minipage}{0.5\linewidth}
\begin{align*}
E &= mc^3 &&\text{Einstein}\footnote{Better check this.}
\end{align*}
\end{minipage}
which yields:

Ok, so that seems to be working.
But wait.. The text of the \footnote duplicated!!! Hmmm, must be the measuring stage that align goes thru. Ok, then that should be easy to fix: all we need to do is to check \ifmeasuring@:
\makeatletter
\newcommand{\AlignFootnote}[1]{%
\ifmeasuring@
\else
\footnote{#1}%
\fi
}
\makeatother
Now using \AlignFootnote{} instead of \footnote{} we get the desired results:

Ok, but in this first use case (Einstein) I just happened to use the \footnote inside the \text{}.
Trying to use \AlignFootnote{} outside of the \text{} (Newton) really screws this up for some reason:

So in the Newton use case, it appears as if the content outside of the \text{} goes thru 4 non-measuring passes.
Attempted Fix:
Well the obvious thing to try was to use \text{\footnote{#1}}, but that not only has no effect on the second use case, it also messes up the first use case: both footnotes show up 4 times.
Questions:
- Main question: Is there a way to detect the repeated passes outside of
\text{}so that I don't have\footnotesduplicated without resorting to\footnotemark/\footnotetext? - Why is the
minipagerequired? Without it the\footnotesdon't show up at all. Is there some flushing type of macro required that would make them show up?
Code:
\documentclass{article}
\usepackage{amsmath}
\makeatletter
\newcommand{\AlignFootnote}[1]{%
\ifmeasuring@
\else
\footnote{#1}%
\fi
}
\makeatother
\begin{document}
\begin{minipage}{0.5\linewidth}
\begin{align}
E &= mc^3 &&\text{Einstein}\AlignFootnote{Better check this.} \
F &= mb &&\text{Newton\AlignFootnote{This also seems wrong for some reason.}}
\end{align}
\end{minipage}
\end{document}



