There are so many it is hard to count.
But the things are always simple.
Most boils down to presentation. Physics is warped, and reality denied in order to make thnigs more emphatic.
The "piff" from a silencer to the "WHAP" from a bare fisted punch. The screeching of tires on asphalt with no smoke, or the fact that doors make the same sound opening and closing throughout the movie (sound "fonts").
Physics, where a car blows up as if the passenger compartment is where they kept the gas, or bending in a way that denies its actual structure. The whole Robert E Lee being able to jump over the same 'Yee-Haw" construction ramp and land, nose down, and still drive off.
Cartoons and sci-fi where one man is able to pick up something large and not fall over because they are not at the center of mass (ok for flyers, but not for strong men). Being able to stop cars by attaching to a bumper or the like (not having them rip off).
Drunks being able to speak better than many sober people I have known.
Gunshots causing people to fly around. Worst example was that linear accelator that supposedly took an aluminum pellet near the speed of light (Arnold flik). The gun was only 5' long, the battery was like a camera bag, and the bullet was aluminum. Instead of evaporating as soon as it hit the air, it flung people around and had no recoil. No straw-thru-the-oak cauterized hole in the target.....
The apartment in NYC ownd by unemployed or recently graduated people that actually has enough room for a couch (Friends, Seinfeld, and a few others that I forget the name).
Bars where you can see EVERY PERSON and hold a conversation w/o shouting.
As for the cloaking, it may be possible. If they can control gravity AND have a warp drive, bending light should not be that hard (gravity does it). You can also just shoot a coherent laser beam in another direction. Light is not like sound. So long as it does not hit somethnig, nobody should see it besides the one you are pointing it at.
There are things that are not realistic, but so long as they do not try to over-explain it is fine. The "Force" is one. When they tried relating it to a "Mitocondiral count" or whatever it was, that ruined it. What is this? DBZ? Blasters are blasters. So long as they do not explain how they work, erroneously, I have no problem.
But the thing to keep in mind is this. So long as you keep to the exceptions you state in the beginning, it is easier to ignore the main fictional parts. If the rest of the world is supposed to be normal, it is easier to accept a few things NOT being normal. The best sci-fi and fantasy have been things where everything else is forced to follow the rules, and something is able to ignore a few.
NOT all of them, but a few.
You can accept Superman so long as he leaves a sonic boom behind him. You can accept his invincible suit so long as regular clothes shred. You can give him laser-vision so long as it does not follow "heat" ot "laser" depending on what the author wants to do with it.
As soon as you start messing with everything, making a throat punch non-lethal, breaking a mans arm and having him able to lift something because he is "strong willed", your mind will already acknowledge this to be fake.
The worst scenes I have seen have not been the most gruesome. They have been the most POSSIBLE.
The hobbling in Misery is one, the ear in Reservoir dogs is the other.
Nuff said.