General Misunderstandings:
* Misinterpret: To understand something incorrectly.
* Misconstrue: To interpret something in a wrong or misleading way.
* Misjudge: To form a wrong opinion about something or someone.
* Misapprehend: To fail to understand something correctly.
* Misperceive: To perceive something incorrectly.
* Get wrong: To make a mistake in understanding something.
More Specific Misunderstandings:
* Confuse: To mix up or mistake one thing for another.
* Err: To make a mistake, often in judgment.
* Misread: To interpret something incorrectly, especially written material.
* Overlook: To fail to notice something important.
* Neglect: To fail to give something the attention it deserves.
* Distort: To twist or change the meaning of something.
Figurative Language:
* Get the wrong end of the stick: To misunderstand something completely.
* Be in the dark: To not understand something.
* Be lost in the fog: To be confused and unable to understand something.
The best word to use will depend on the specific context of the misunderstanding.