This MWE fails to compile the first time you run pdflatex on it, but works every time after that.

[Canageek]

\documentclass{article}
\usepackage{chemnum}
\begin{document}
\cmpd{peroxo.meoh} \cmpd{peroxo.etoh} \cmpd{peroxo.ppn} \refcmpd{peroxo.{meoh,etoh,ppn}}
\end{document}

Gives the following error:

! Missing number, treated as zero.
<to be read again>
                   \__int_eval_end:
l.4 ...eroxo.ppn} \refcmpd{peroxo.{meoh,etoh,ppn}}

However, if you hit r, then run pdflatex again, it compiles fine.

[Canageek]

Ulrike Fischer has found a workaround:

\usepackage{chemnum}
\ExplSyntaxOn
\cs_set_protected:Npn \chemnum_sort_subcompounds:NNNnnNN #1#2#3#4#5#6#7
  {
    \seq_clear:N #6
    \seq_clear:N #7
    \bool_if:NF #1
      {
        \seq_if_exist:cTF {g__chemnum_compound_#5_subcompounds_seq}
          {
            \seq_map_inline:Nn #3
              {
                \seq_if_in:cnTF {g__chemnum_compound_#5_subcompounds_seq} {##1}
                  {
                    \seq_put_right:Nn #6
                      { \chemnum_write_subcompound:NNnnn #1 #2 {#4} {#5} {##1} }
                    \bool_if:NTF #2
                      {
                        \seq_put_right:Nx #7
                          {
                            \int_eval:n{0\chemnum_expandable_get_subcompound_property:nnn
                              {#5} {##1} {previous-number}}
                          }
                      }
                      {
                        \seq_put_right:Nx #7
                          {
                            \chemnum_expandable_get_subcompound_property:nnn
                              {#5} {##1} {number}
                          }
                      }
                  }
                  { \__chemnum_nothing_here:nn {##1} {#5} }
              }
          }
          { \__chemnum_nothing_here:xn { \seq_use:Nnnn #3 {,~} {,~} {,~} } {#5} }
      }
  }
\ExplSyntaxOff

[cgnieder]

Thanks. Fixed for the next update.