This is a typo in the manual (which I have fixed for the next release). In the $derivative_coupling section you specify which states you want, with 0 indicating the reference state and 1,2,3,… being the excited states. You then get the couplings between all pairs of states that are indicated in the $derivative_coupling section. This is clear if you look at the output, because the energies of the individual state are listed as Ei and Ej, e.g.:
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CIS Derivative Couplings
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between states 0 and 1
NCharge is 0
get_w_dc time: CPU 0.60 s wall 0.14 s
AOints 129 time: CPU 0.94 s wall 0.21 s
DFT time CPU 0.62 s wall 0.12 s
Ei = -78.585544
Ej = -78.268659
Ej-Ei = 0.316886
and in this particular example (which is Example 9-218 in the manual) you should be able to identify Ei as the ground-state energy (state index 0) and Ej and the S1 energy (state index 1). Output (including the derivative couplings that are printed next) is in atomic units.