That one had me puzzled for a minute... The solution is to match your brackets: both terms should have an additional }
to close the argument of the outmost derivative. So
\partial{#}::PartialDerivative;
c1:= \partial_{\alpha}{\partial_{\beta}{h_{\mu \nu}}} =
\partial_{\beta}{\partial_{\alpha}{h_{\mu \nu}}};
And to answer the question in the subject: you can then make these terms equal with a call to canonicalise(c1)
.