Aerial Knock-back Projectiles
This factory flaw allows you to execute an aerial projectile after you've been knocked-back when reaching the maximum hit limit of 4 hits. This has been addressed and no longer is a problem in MK2+.
The "Death Punch"
With a perfectly timed press of the high punch button while an attacker jumps towards you, you can nail them with a 5-hit / 33% punch. This has been addressed as well and is no longer a problem in MK2+.
Have you ever noticed when you do Jax's arm rip fatality on Raiden that he is given Kung Lao's arms? Was it a mistake? Possibly, but with no evidence of Raiden having his own arms I believe this was intentional as a last minute "fix".
Head Snack Floor Scroll
If you have ever performed Reptile's 'Head Snack' fatality on the stage 'The Armory' then you will know about this factory bug. The floor starts to scroll as the opponent falls to the ground. As you can see from the video, this too has been fixed in MK2+. This bug was due to an error in data-sized being copied to memory.
Kung Lao's Headbutt
This problem is most evident against Mileena. As you can see in the before image the hit box is strangely shaped and a bit short. The 2nd image shows the change and is more consistent.