Apologies: I originally misunderstood your question.
In singular _cubical_ homology, degenerate cubes are cubes that are constant in one of the coordinates.
The group $C_n$ is defined to be the _quotient_ , $$ C_n = \frac{Q_n}{D_n}.$$ This is the appropriate relationship between $Q_n$, $D_n$ and $C_n$.
From the way your question was asked, I would assume that you were thinking of the elements in $C_n$ as cube chains. They are not. The elements in $C_n$ are _equivalence classes_ of cube chains, modulo some degenerate cubes that you ignore.
Note that the boundary map $\delta_n$ sends $D_n$ into $D_{n-1}$, which ensures that $\delta_n$ descends to a well-defined map from the quotient $C_n$ to the quotient $C_{n - 1}$.