I have some pipe tables with some long rows and when they get converted to LaTeX, the columns widths add up to more than one, resulting in the table extending into and beyond the margin of the page.

I can reproduce the behavior for even a small table with the --columns argument set small enough. For example, if test.md is:

| test  | header | row    |
|-------+--------+--------|
| first | row    | elemnt |

Then running

pandoc test.md --columns=12 -t latex

yields

\begin{longtable}[c]{@{}lll@{}}
\toprule
\begin{minipage}[b]{0.61\columnwidth}\raggedright\strut
test
\strut\end{minipage}
&
\begin{minipage}[b]{0.68\columnwidth}\raggedright\strut
header
\strut\end{minipage}
&
\begin{minipage}[b]{0.68\columnwidth}\raggedright\strut
row
\strut\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.61\columnwidth}\raggedright\strut
first
\strut\end{minipage}
&
\begin{minipage}[t]{0.68\columnwidth}\raggedright\strut
row
\strut\end{minipage}
&
\begin{minipage}[t]{0.68\columnwidth}\raggedright\strut
elemnt
\strut\end{minipage}\tabularnewline
\bottomrule
\end{longtable}

where the columns widths in a row sum to more than one \columnwidth. In fact, narowing the
--columns make the problem worse:

pandoc test.md --columns=10 -t latex

produces

\begin{longtable}[c]{@{}lll@{}}
\toprule
\begin{minipage}[b]{0.73\columnwidth}\raggedright\strut
test
\strut\end{minipage}
&
\begin{minipage}[b]{0.82\columnwidth}\raggedright\strut
header
\strut\end{minipage}
&
\begin{minipage}[b]{0.82\columnwidth}\raggedright\strut
row
\strut\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.73\columnwidth}\raggedright\strut
first
\strut\end{minipage}
&
\begin{minipage}[t]{0.82\columnwidth}\raggedright\strut
row
\strut\end{minipage}
&
\begin{minipage}[t]{0.82\columnwidth}\raggedright\strut
elemnt
\strut\end{minipage}\tabularnewline
\bottomrule
\end{longtable}

Thanks @jgm! Tables look great after this change!