Something else that I've been having trouble with is this:
there seems to be a lot of homophones (words that sound the same but are spelled differently and mean different things; an example in English would be blue and blew) in Japanese.

Example:
加, 蚊, 課, 科, 可, 佳, 戈, 乎, 架, 日, 化, 顆 and 仮 can all be pronounced the same way - ka. To someone new to the languge (like me) that can be a bit confusing at first. (Viz. - when someone says ka in a sentence, which of those kanji is it? It's only something experience will tell a person.)