Siunitx, exponent-to-prefix, square

The exponent-to-prefix conversion is quite 'simple minded' and is meant for easy-to-handle cases. Initially that meant that the behaviour with power in units was undefined. However, it is simple to extend the conversion code for the case

\SI{0.001}{\metre\squared}

or similar. This has therefore been done and will be present in v2.6o onward (sent to CTAN 2016-01-05).

siunitx just provides \squared as a notation macro, not a computation. So 0,0001 metre is (correctly) converted to 100 micrometre and the square symbol is added, resulting in 100 μm². Cf.

\documentclass[fleqn]{article}
\usepackage[per-mode=fraction]{siunitx} % also loads xparse and expl3
\begin{document}
\SI{5}{\metre\squared}
\end{document}

which gives 5m² (and not 25m²).