WordNet sense 1 (cause annoyance in; disturb, especially by minor irritations):

annoy, bother, chafe, devil, gravel, irritate, nark, nettle, rag, rile, get at, get to

WordNet sense 2 (disturb the peace of mind of; afflict with mental agitation or distress):

worry

WordNet sense 3 (change the arrangement or position of):

agitate, disturb, commove, shake up, raise up, stir up

WordNet sense 4 (be a mystery or bewildering to):

amaze, baffle, beat, bewilder, dumbfound, flummox, get, mystify, nonplus, perplex, pose, puzzle, stick, stupefy