I can't quite get my head around the difference between misapprehension and its opposite apprehension.
I understand the latter, but the former still eludes me.
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Apprehension is not usually used as the opposite of misapprehension.
Misapprehension is another word for misunderstanding - "A mistaken belief about or interpretation of something".
Apprehension can mean "understanding", but is usually used to refer to a feeling of fear or misgiving about a future event.
"Misapprehension" only negates one meaning of "apprehension":
misapprehension — a mistaken belief about or interpretation of something
apprehension — understanding; grasp
The other meanings of apprehension are generally not relevant to the meaning of misapprehension.
Usage examples from the same dictionary I grabbed the definitions:
the pure apprehension of the work of art
she must have been laboring under the misapprehension that you are nice