This is very common in the game , at least in the Sega version, when you use Sindels hair attack fatality, the hair will exceed the height of the person and will glitch., This is true especially when you face off against taller opponents and it doesn't line up properly.
One of the points of the original Mortal Kombat games is that Liu Kang is the chosen one, and is Earth's champion. The games seem to gloss over the fact that many of the earth warriors in the game and especially Mortal Kombat 3, have good endings. It make no sense that Liu Kang is the chosen one. It could have been any earth warrior who choose to win the tournament. So why does it have to be Liu Kang??? Even some of the villains in the game have good endings, so why does it matter who wins, as long as earth does.
Shang Tsung can appear twice in the game, this is very obvious and often happens. Yet, if you fight him the first time and kill him, he will come back without explanation. This is common in the Sega Version, and generally happens when you choose the highest difficulty and A Earthrealm warrior. This is never explained, and there is no explanation for his sudden resurrection.
Were do Scorpion, Mileena and Baraka go??? They all seem to disappear without explanation, and there is no explanation as to why this happens. It possible they could have been killed in the last game, but almost all of them are seen in Ultimate Mortal Kombat and it's expansions, so there sudden reappearance is not explained and no answer is given as to why there were gone in the first place.
In Mortal Kombat 3, the one were Nightwolf sends light at a rival character and turns them into ash, sometimes the fatality will mess up and a mistake with the lighting, as Cyrax, and Sektor will suddenly start to glow and change colors. This is in the Sega Version.
One of the aspects of the game is that SubZero is supposed to be being hunted by all of the cyborgs in the game. Yet, if you spare him, are the fatality timer runs out, the game still treats the endings as if you killed him. Creating not only a plot hole, but that ending makes little sense.
One of the key plot points of Mortal Kombat 3 is Shao Kahn uses Sindel to open the portals to Earth, and the Earthrealm warriors must stop her and Kahn. Yet, it's never explained when you beat Sindel early in the game, why the portals don't close after you beat her. Kahn didn't have the ability to keep them open, and upon her death as dark as it is, the game should have been over and earth saved. This is not explained and is a huge plot hole.
In the ending that features Cyrax, after winning the tournament and beating Kahn, he is reprogrammed and sent into the dessert, to a goal he never reaches and he malfunctions there. Assuming this could be considered a cannon ending, it would have been smarter for the Earthrealm warriors to reprogram him to be a on the side of Earth. Not only was he strong enough to defeat Kahn, a formidable villain in his own right, he was able to defeat many Earthrealm warriors and Kahn's warriors in the Mortal Kombat contest, and even kill them. Kahn has tried dirty tactics before, and would certainly try again, or another empire from one of the other realms would try to invade Earth. Some why not reprogram Earth's Champion, and make him one of Earth's warriors, and give themselves a advantage. This makes no sense.
In NightWolfs ending, after beating Kahn in the tournament, he receives a lot of respect,gets his ancestors land back, and becomes Earths Greatest Warrior. Yet, this does not seem to happen if you don't get NightWolfs ending. Not only is this a big plot hole, it is never explained in subsequent games if this still happened. It's like the entire series, just glosses over this. It's not even mentioned in later games, it's like it didn't happen and was forgotten about.
When you play as any of the Earthrealm Warriors in the game, you can kill or murder other earth warriors. This does not make any sense, as the original continuity of the series there were in alliances with each other, and the game should have prevented them from doing so, but you can kill what could be army to fight against Kahn and his forces. This absolutely makes no sense, yes you can use friendships and spare them in the fight, but you should have never had the option to kill your allies in the first place.