General:
* Bewilders
* Disorients
* Mystifies
* Puzzles
* Perplexes
* Baffles
* Stumps
* Befuddles
* Ambiguates
More specific:
* Misleads (implies incorrect information)
* Misinterprets (implies misunderstanding)
* Muddies (implies making something unclear)
* Obscures (implies making something hidden)
* Clouds (implies making something uncertain)
Informal:
* Throws off
* Trips up
* Gets to
* Mixes up
The best synonym will depend on the specific situation and the intended meaning.