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You must not insert additional returns. Extra newlines will ruin the table. If you need a space use

%

on the line (so it becomes a comment, not just a newline)

\usepackage{ctable}

\ctable[cap = {TABLE CAPTION},caption = {ninny},label={idiottable},]{cc}
{
  % You specify table footnotes here.
  \tnote[$\ast$]{DA FOOTNOTE 1}
  \tnote[$\dagger$]{dat other footnote}
  \tnote[b]{mistakes are possible (you must match these up yourself)}
}{
\FL % FLORIDA (just kidding, means "first line")
COL 1\tmark[a] & COL 2\tmark[$\ast$]
\ML % middle line
6.920e+00\tmark[$\dagger$]     &   0.09781\\
97     &   2000
\LL % last line
}

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