documentclass{article}
usepackage{xcolor}
usepackage{colortbl}
begin{document}
Workspar
begin{tabular}{ll}
  rowcolor{red!20}%
  rowcolor{blue!20}%
  A & B
end{tabular}

Doesn't workpar
begin{tabular}{ll}
  rowcolor{red!20}%
  % Uncomment line below to get the unexpected behavior
  %input{mwe-bit.tex}
end{tabular}
end{document}

rowcolor{blue!20}%
A & B

! Misplaced noalign.
rowcolor ->noalign
                     {ifnum 0=`}fi global let CT@do@color CT@@do@color...
l.1 rowcolor
             {blue!20}