Let $M$ and $N$ be differential graded (DG) modules over a positively graded commutative DG algebra $A$. We show that the Ext-groups $operatorname{Ext}^i_A(M,N)$ defined in terms of semi-projective resolutions are not in general isomorphic to the Yoneda Ext-groups $operatorname{YExt}^i_A(M,N)$ given in terms of equivalence classes of extensions. On the other hand, we show that these groups are isomorphic when the first DG module is semi-projective.