Safety
Lasers generate a lot of heat and can also create sparks and even toxic fumes. In addition to the thermal stress the material undergoes, the worker is at much greater risk.
Composition
Lasers work well for cutting non-reflective metals, plastic, and more, but waterjets are much more efficient to cut a combination of materials with different melting points.
Shape
Objects that are thicker or have a varying height do not work as well with lasers as flat sheets do. Waterjet cutting precision can make this process much easier and faster.