Sometimes the function ConjugacyClasses in version 3.4
gives a wrong answer when applied to permutation groups
of order >1000. As it seems, only rational classes are
considered:

gap> G:=Group((1,2,3,4,5), (1,2,3), (6,7,8,9,10), (6,7,8));;
gap> Length(ConjugacyClasses(G));
17