In a way that confuses or causes confusion; in a manner that is unclear or bewildering.
From confusing (present participle of confuse used as an adjective) + -ly (manner adverb). Confuse comes from Latin confundere; -ly forms adverbs from adjectives.
The word 'confusingly' gets extra ironic when used in instruction manuals—'Confusingly, the left button actually turns off the device'—because the writer is literally acknowledging that they're describing something illogical that the user might not understand.
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