I feel your pain OP.
Same exact thing happened to me. Looted Xeno in 16-man Story Mode and didn't receive my helixes. I did get the Gree reputation item though. I submitted a ticket on this as well but it would be nice to get a response other than the "Thank you for playing SWTOR! Unfortunately, we can't help you!" (I assume this will happen, pretty typical when I submit a ticket.)
I did get my helixes from HM 16-man Xeno though. And NO I did not forget to loot the boss afterwards.