My son and I both have '08 SD's that we bought together, same day same dealership. Recently he noticed a fairly drastic drop in gas mileage, but knew he'd be installing his new CPR Rottweiler system and his Tune ECU goodies so that would be a good time to check the vitals. Turns out that one of his velocity stacks (still in the yet untouched stock airbox) had backed out and was bouncing around on the throttle bodies.

We are both installing the RC8 stacks, so I opted to safety wire mine in after the install. Has anybody else had this issue? Or, is it just a fluke?

Never heard of that. They click in with a plastic tab and when the O-ring type gaskets or original air filter is put in properly it is quite tight.
My guess is that someone who swapped filters or so didn't put them in properly. (not saying it's you, could be at the dealer)

I had the same issue. Stock untouched air box, went to do a valve check and found one of them laying down horizontally with a shit ton of the air filter material in the throttle bodies.

When I fitted the RC8 stacks I found that the clip features that locks the stacks in place were not properly engaging. They stacks are a tight fit and hard to turn without lubrication but I slightly modified the clip angles to make them easy to twist/snap on. Maybe the person who originally fitted these stacks twisted them on but not far enough to engage the snap feature - or didn't realise there is one. If so they could easily have vibrated round and fallen off. Lockwire is not a bad idea really.