These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Kahn kills Rain for not making his enemies beg for mercy before dispatching them. Why he would kill a general whose troops just offed two of Earth's best warriors for that reason is baffling. The closest you get is Rain quickly saying "But master, I thought if I let them live-" before being cut off, but that could mean anything.
It could also be interpreted as an echo of the earlier scene where Shinnok asked Kahn if he'd made Raiden beg for mercy before killing him; Kahn, knowing that neither happened, was hesitant to admit that failure to Shinnok. In the same way, Rain merely said that Kabal and Stryker were "taken," meaning possibly that they were captured, not killed; Kahn's expectation was that they should have been killed, and when Rain admits that this wasn't the case, he was killed for showing mercy.
Why are the heroes taking Kahn's seven-day deadline at face value? Wouldn't that have been a shock to them if Kahn showed up on Day 4 instead?
Fridge Horror to add to this: Everyone, including Kahn himself, was saying that the seven-day deadline was necessary for the realms to completely merge and for Outworld to be totally victorious; however, Kahn could just as easily have struck on any day prior to Day 6, especially since there's not much indication that that much time has passed between Kahn's initial appearance and the heroes' arrival in Outworld (the most we see is the change from day to night to day from Kahn's first arrival to when Sonya finds Jax, but that would mean only two days have passed, and we don't know how much time has passed since the latter point)—he just did it this way to screw with Raiden, who it's established loses more of his powers the longer the merger goes on.
Why didn't Raiden kill Kahn's army after Johnny Cage is killed? He seemed as if he had the power to do so when preparing to exchange himself to Kahn.
For that matter, why didn't Raiden just kill Kahn himself during their initial fight? He waswiping the floor with Kahn after the initial surprise strike-down Kahn gave him, and only started sharing the Idiot Ball with Sonya when Kahn roped her legs and dragged her into Distressed Damsel mode.
Pandering to the Base: Annihilation vomits new character after new character at the audience in an attempt to fit in all the new arrivals from Trilogy and earn some cred from the faithful. General feedback on the movie should be an indication of how well this worked.
Plus the... flying creature that emerges from Shao Kahn's body after he's beaten. Neither it nor the body husk it leaves behind is any believable.
On a related note, the gargoyle that appears is arguably either the film's best effectnote which is saying a lot, or is worse than either of the creatures in the aforementioned fight scene.
When it grabs Sonya at one point, she too becomes a rather obvious CGI double.
Ermac's mask falls off during the fight between him and Sonya. This bit occurs when the latter grabs the former's head with her legs.
A similar event happens during the fight between Scorpion and Sub Zero. Only this time, it occurs when the former catches the latter.
When Liu Kang does his flip kick, there's a visual flash of when he kicks the camera.
Rain gets knocked into a flaming pit by Shao Kahn. When Baraka gets knocked towards the same pit, we see... Rain falling in again.
There are cables visible all over the place, but none more noticeable than during Scorpion and Sub Zero's fight.
Motaro's front legs are obvious human legs with human feet instead of horse legs with hooves.
In other words, pretty much everything. Even the titles are bad by virtue of reusing the titles from the original movie, as explained below.
They Just Didn't Care: They use the exact same title sequence than the first film, with the only change being that the letters of "Mortal Kombat" flip to reveal the subtitle. What's more, they reuse clips from the first movie in several places.