I have had this happen to me, Hexx, but very, very, VERY, rarely. Likewise, I've rarely had plasma torps slam into my target and deliver zero damage. That's really inconveniant, especially when the target is still fully-armed.
I'm guessing it's the same bug in both cases.
The one thing I have noticed is that once this bug starts, it lasts for the duration of the entire mission. Therefore, whenever it happens to me now (which is probably less than one mission in 500) I simply bug out.
-S'Cipio