We're landing in "used" instances, not unlike the old bug where you would warp in to a completed STF.
Devs didn't catch this in their testing because not enough of them were playing at the same time to actually land their character in a "used" instance before it got garbage collected.
This is also why you sometimes don't encounter the bug after changing characters for a while, deleting and remaking the character, and logging off for a while: All of these actions take long enough so that you cannot return to the instance you left. And if you're lucky, the game will create a fresh, new instance for you and everything will be fine.
Some scripts (the whole crashed shuttle bit, for example) appear to trigger from the act of progressing. Other scripts, however, seem to rely on the map's state, and can't be triggered if the mission has ever gone past that point.
Because of this, it's possible to get past the rifle bug by changing instances to a zone that stopped progressing BEFORE that part of the mission for somebody else. But it will only work once; a second person can't come in after you leave and get their bug fixed, too.
For example, if you land on the planet and see, for no reason, Dr. Muller standing next to your shuttle with a phaser rife, that's a leftover from the end state of Tarus II. That means you're going to hit the Rifle Bug. And everything else that relies on the state of the mission/map.
TL;DR: If anybody in the instance before you were progressed the mission BEYOND the rife equip portion, the game STOPS CHECKING for the equip and your mission tracker won't make it restart.
Devs didn't catch this in their testing because not enough of them were playing at the same time to actually land their character in a "used" instance before it got garbage collected.
This is also why you sometimes don't encounter the bug after changing characters for a while, deleting and remaking the character, and logging off for a while: All of these actions take long enough so that you cannot return to the instance you left. And if you're lucky, the game will create a fresh, new instance for you and everything will be fine.
Some scripts (the whole crashed shuttle bit, for example) appear to trigger from the act of progressing. Other scripts, however, seem to rely on the map's state, and can't be triggered if the mission has ever gone past that point.
Because of this, it's possible to get past the rifle bug by changing instances to a zone that stopped progressing BEFORE that part of the mission for somebody else. But it will only work once; a second person can't come in after you leave and get their bug fixed, too.
For example, if you land on the planet and see, for no reason, Dr. Muller standing next to your shuttle with a phaser rife, that's a leftover from the end state of Tarus II. That means you're going to hit the Rifle Bug. And everything else that relies on the state of the mission/map.
TL;DR: If anybody in the instance before you were progressed the mission BEYOND the rife equip portion, the game STOPS CHECKING for the equip and your mission tracker won't make it restart.