What could cause a quadrature encoder to produce this output?
It may just be cheap. Rather than setting the phase accurately as WhatRoughBeast says, the engineers who designed this one may have just said "Well, you can find speed and direction from this, good enough!"

The schematic shows that both phototransistors are part of the same package, so they may just be oriented in a way that they pick up the transitions in the expected order, not worrying about phase.