It is pretty much a given that Hollywood is going to get science, tech, and details about culture and subcultures wrong much more often then they get them right. Part of this is because of what is referred to as the 'coconut effect', though others are just because most people with knowledge of things other than writing will go into fields other than writing.
Here's a list of some things that bother me that I don't believe have been mentioned yet.
-Ninjas wearing dark black clothing. Even at night, wearing black will get you spotted without too much difficulty. Often for stealth plain clothes work best, because people are usually among other people, and most people wear plain clothes and not Hollywood-Ninja-Stagehand costumes. Well at least they are not...
-Ninjas wearing very obvious clothing. Orange jumpsuits and other such things.
-The idea that magic has to be unexplainable, if magic violates scientific principles that we are accustomed with, that is fine, but don't say that because something is magic it can just blindly violate any law, theory, or theorem that it wants.
-On that note: Science is not the opposite of magic, you can apply science to magic and it can easily still be considered magic. The two are not at ends, and the idea of scientists and magicians being warring factions is absurd.
-I just generally don't like how Hollywood handles magic. Even characters that are supposed to be cunning only use magic for straightforward attacks. That is, the magic tends to be impractical, and used inefficiently and uncreatively. For example: Fireballs.
-Hypotheses, Laws, Theories, and Theorems are not to be confused with each other.
-Scientists are not overzealous people unable to even consider implausible things. Likewise, not all scientists are atheists/nihilists/misotheists. It is blatantly unscientific to blindly dismiss things, however Occam's Razor tends to be applied.
-One last thing, because this is starting to get way, way too long: Occam's Razor. Characters in Hollywood movies and shows often tend to jump to absurd conclusions, and be correct to boot, with little or no explanation of how or why they reached such a conclusion.