there are some cast on ons that cause the yarns to twist.. (Braided long tail come immediately to mind)
there are other cast ons that cause a single strand of the cast on yarn to twist...(standard long tail)
When working with 2 strands of yarn, held together, these will twist, (because the motion of the hands is always in the same direction) but it doesn't matter!
if it bothers you, you can untwist by holding the yarns (on in each hand, letting the knitting (work) dangle and untwisting the yarns (the work will spin!)
If the twist is just in the cast on, well that's soon done with!