beamer: Footnote in columns Environment | Indention Too Short

Playing with your MWE, I discovered that columns doesn't really handle footnotes (doesn't force them to keep the column size and also causes the problem of your question)

This is the way I found that it works better:

documentclass[t]{beamer}

begin{document}

begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{column}{.50textwidth}
        begin{itemize}
        item Text Text Text.footnotemark[1]
        end{itemize}
        end{column}
        %
        begin{column}{.50textwidth}
        begin{itemize}
        item Text Text Text.
        item Text Textfootnotemark[2]
        end{itemize}
        end{column}

    end{columns}
        %
footnotetext[1]{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
footnotetext[2]{This is Two: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
end{frame}
end{document}

If you want separate footnote place for each column, this answer doesn't help you... And may be I can try for another way... But it is ok for my taste.

Output:

PS: may be we have to reduce a little bit from 0.5 (but I am not sure if columns use a inner or outer sep... so didn't do it yet)

Edit A fix but with not original indent of footnote:

I created the footcolumn to be used when footnotes are included instead of the original:

documentclass[t]{beamer}
usepackage{adjustbox}
letoldfootnotetextfootnotetext
newsavebox{mybox}
deffootnote#1{footnotemark[1]oldfootnotetext[1]{adjustbox{valign=t}{begin{minipage}[b]{0.9textwidth}#1end{minipage}}}}

newenvironment{footcolumn}
{begin{column}}{end{column}hspace{-0.5textwidth}}

begin{document}

begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Text TextText.footnote{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Text Text Text.
        item Text Textfootnote{This is two: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}

    end{columns}
        %
end{frame}
begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Test
        item Text TextText.footnote{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}
        %
        begin{column}{.50textwidth}
        begin{itemize}
        item Text Text Text.
        item Text Text
        end{itemize}
        end{column}

    end{columns}
        %
end{frame}
end{document}

Output:

You can combine it with the original without problems (even as last column will work ok!). It is not perfect, because of the non indented start.. But Closer I think.

Last Edit before remove previous:

(Fixed some indent)

documentclass[t]{beamer}
usepackage{adjustbox}
letoldfootnotetextfootnotetext
newdimenmyindent
myindent=2mm
newcounter{myfootnote}
makeatletter
deffootnote{stepcounter{myfootnote}xdefthemyfootnote{arabic{myfootnote}}@ifnextchar[{readFootnoteNum}{readFootnote}}
defreadFootnoteNum[#1]{footnotemark[#1]xdefthemyfootnote{#1}addtocounter{myfootnote}{-1}readFootnote}
defreadFootnote#1{oldfootnotetext{adjustbox{valign=t}{begin{minipage}[b]{0.86textwidth}hspace{myindent}$^{themyfootnote}$#1end{minipage}}}}
makeatother

newenvironment{footcolumn}
{begin{column}}{end{column}hspace{dimexpr-0.5textwidth+myindent}}

begin{document}

begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Text TextText.footnote{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Text Text Text.
        item Text Textfootnote{This is two: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}

    end{columns}
        %
end{frame}
begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Test
        item Text TextText.footnote[90]{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        end{itemize}
        end{footcolumn}
        %
        begin{column}{.50textwidth}
        begin{itemize}
         item Text Text Text.
        item Text Text
        end{itemize}
        end{column}

    end{columns}
        %
end{frame}

begin{frame}
%
frametitle{Title of Frame}

    begin{columns}[t]
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Testfootnote{Test here}
        item Text TextText.
        end{itemize}
        end{footcolumn}
        %
        begin{footcolumn}{.50textwidth}
        begin{itemize}
        item Text Text Textfootnote{This is one: Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text Long Footnote Text}
        item Text Text
        end{itemize}
        end{footcolumn}

    end{columns}
        %
end{frame}
end{document}