I have not experienced this...I have the PS2 version, so I'm not certain whether or not this glitch is in that port.
And speaking of "Orochi Glitches", I came across another one.
Normally, in boss fights where it's the boss and a few regular enemies against you (ie, the Mileena fight in the Living Forest, where she has a couple of masked guards with her), as well as boss fights where it's just the boss/bosses against you, the fatality stunner is disabled, and for the bosses that have been in previous MK games such as MK2, you can only use the fatality stunner against that boss when his/her health is depleted and use a specific input to execute a certain fatality on them (exceptions are the initial Kitana fight, and the Mileena Living Forest fight).
This particular boss fight, however, the fatality stunner is not disabled. This holds true in both the Soul Tombs AND the Foundry. First, hit the other enemies with the fatality stunner (Tarkata in the Soul Tombs, Demon General in the Foundry), and execute your brutality input. And, you can actually hit the Orochi Hellbeast during the time you have to pull off your brutality stunts. Not only that, but with your brutality, you can kill Orochi literally within about 10 seconds. My first encounter with Orochi only took that amount of time to finish.