"Liu Kang does 6 bicycle kicks in a row and then does his default 7 hit dialin combo. This does 100%+ damage and he ends up on your opposite side. Looks funny. Have you ever seen that?"
The CPU can do multiple bike kicks because it doesn't have to charge the move, however, if it was a command move, a person could do that too since you can do an attack after a Bike Kick and have it combo unblockably so long as you interrupt one of their attacks with the Bike Kick itself. Try vs a person, do a Bike Kick, have P2 Roundhouse and get hit midscreen, then afterward do a LK. P2 will not be able to block it, then try it with a naked Bike Kick, P2 will always be able to block. Same goes for his 7 hit combo in the corner after a counter Bike Kick. You can also do an unblockable ducking LK or sweep after his corner combo with the right timing because of "must land" properties after autocombos". Generally, once a character touches the ground, they can block, but specifically not after autocombos. There are other instances where you can connect a hit in air on the last frame the game perceives them as airborn, and on the very next frame where it registers the hit, they will be standing on the ground.
"Using Nightwolf to reflect Subbys freeze. Do this combo. HK, HP, HP, LP, Hatchet, Hatchet, the walk forward and do a third Hatchet. The last Hatchet isn't even part of the combo yet it registers."
It is part of the juggling section of his combo, and is part of any official combo so long as they do not touch the ground. It is possible after that third axe, to run in, LP, and do a fourth axe. It is easy to perform a blockable but comboable infinite of all axes on the Robots across the full screen distance because of their collision detection. In the corner vs the Robots, Sheeva, Kabal, and Kano, it is possible to perform an infinite with Nightwolf's 3 hit kick combo because of the "must land" property in autocombos, the quickness of his 3 hit kick combo's recovery, and said characters' collision detection. It is however, not possible to combo off the ground after his axe since the axe does not have a "must fall" property.
"You can't throw any computer opponent that is caught in Cyrax' Plasma Net. Instead, they throw you. That's impossible."
There becomes a point in UMK3 1.2 difficulty level where you cannot throw the CPU at all. They can cancel any of their special attacks or recovery frames with a throw, like Jade's dash kick for example. It is not limited to Cyrax's net, however you can always throw the CPU out of Sub-zero's freeze. On other containments throwing in general is disable even in 1 on 1 gameplay, like the Spear. If you could throw the CPU all the time, they would have had to program in a cpu concept for "holding back" since holding back prevents you from being thrown. Had they not bothered with that and made it so the CPU had no way to prevent throws, some characters could just repeatedly throw the CPU and be very easy to beat the game with. It would have caused a huge amount of problems with the already terrilbe AI and I completely understand why they did it.
"I have seen two Cyrax Plasma Nets onscreen at once."
CPU has no special move limits. They can do multiple teleport uppercuts in a row, multiple spins while you're still spinning with Kabal (which you mention), constant spamming Kitana fan throws. All of this exists in previous MKs in one way or another.
"Not a glitch but worth mentioning here. When fighting Shao Kahn using Sektor, you can double teleport punch him. Why can't Sektor do that to any other characters?"
That is a glitch, you shouldn't be able to do that. It's almost like a CPU programming overflow the human control. Like Dave said Kung Lao can spin infinite bosses in the corner, just the spin, no hits inbetween. Same glitched property. Also, the spin normally activates damage protection in UMK3, but against the bosses, it doesn't. The damage vs them is lower, but it doesn't change.
"Sonyas dialin combo rarely finishes when fighting Shao kahn. Why's that?"
Collision detection and recovery time. Also, bosses can block at any time during autocombos, even under human control in MKT. MK3 is a little different in the sense Motaro and Shao Kahn release block mid combo all the time.
"How come when you miss a combo, Sheeva will always take full advantage and do who most damaging combo, yet Kabal doesn't. Why is that?"
After the CPU does a pop up combo, they generally stand in place because they aren't programmed to do a bread and butter combo afterward. Sheeva is programmed to do her 7 hit in this situation. For Kabal to get the most damage out of a ground combo, he would have to do his 4 hit kick combo. To get the best combo to juggle, he would have to do something the programmers weren't able to do when by the time the game was finished.