When I was teaching about ancient Greece, my students kept calling Socrates, "So-Crates" and at first I laughed but when it persisted it became really annoying.
EDIT: Grammar
When students begin their papers with, "Since the beginning of time," or "Throughout history..."
Annoying:
Mistaking knowledge of dates and very specific facts for being "good at history" whilst being unable to see the wider scope, historical context, controversies...
Funny:
"Immanuel Kant was the inventor of Mer-Kantilism"
"There is a lack of peaceful intercourse between Israelis and Palestinians"
"Remolus and Romus were conceived by a wolf"
"The medieval peasants were at the bottom of the food chain"
Neither annoying or funny, but the biggest misconceptions I see, and this is nearly ubiquitous, is that the point of a history class is to make vague, moralizing statements that create a narrative of progress leading happily and inevitably to today. If people in the past seem to be changing so that they are more like us, this is Progress and it's Good. History is also full of Bad People who do Bad Things, but happily those people are all dead now and those Bad Things don't exist anymore--except the things that can be easily reduced to moral claims, like Greed. People have been Greedy since the Beginning of Time.
As you can imagine, this makes teaching analysis difficult. Students want to judge, not understand. Or, rather, I think in their minds judging and understanding are pretty much the same thing.
Edit--The other big thing, of course, is not following directions. But, I think this is related to the thing above. Students are both poor at close reading and comprehension, and conditioned to be risk averse; their habits are therefore very tough to break. They've done this before and always did fine, so they'll just keep doing what they've been doing. They almost don't believe you when you give them directions they're unaccustomed to.
I feel bad for my junior year HS teacher since I thought Europe was spelled urape and I must have written that on tests a million times. In hindsight it was very embarrassing, probably for the both of us.
Mata Hari "He was a Russian spy." ... Okay, the gender thing, meh. You've missed the point, but WRONG SIDE OF THE WAR.
Most annoying is the style of argument we in Northern Ireland call "whataboutery" so that in response to a question such as "To what extent was the IRA a terrorist organisation?" You got an answer along the lines of " even if they were, what about all the terrible things the British army did..."
Funniest was the essay that claimed the main source of conflict between the Vikings and the native Irish was that the Vikings were Protestant and the Irish were Catholic.
Annoying: confusing knowledge with intelligence and using that to justify people in the past not knowing things or making what seem to be poor choices.
Funny: calling a 'scape goat' an 'escape goat.' It always makes me picture a goat with lightning bolts shaved into the sides. "Oh no! I did something wrong! Quick! To the escape goat!"
Spelling:
(The misspellings of less practiced things in my field, I don't sweat over so much, but of words/names common in English? Yes.)
Word Construction:
Then there's the rampant misuse of certain elements of punctuation, especially semicolons. Please, for the love of language, can we ban the use of semicolons until the writer passes some kind of competency exam?
I'll leave out the conceptual stuff which, while annoying, at least serves the purpose of exposing the people who haven't been in class or paying attention to the readings. It saves me from needing an attendance policy, but it's infuriating to read about timeless tribes and backwards Africa when much of the term has involved subjects and discussions very much incompatible with such an archaic view.
Isn't the So-crates pronunciation an old British thing?