Although chinchillas' urine is usually yellow, the color can vary from yellow to orange/brown. I think in most cases orange/red urine is produced when porphyrins (pigments that are abundant in nature) are excreted in the urine, and the urine darkens to an orange/brown after exposure to light; may also depend on the amount/conbination of plants your chin consumed.
Another possibility is the urinary excretion of synthetic iron or B vitamins.
I'd make sure that the water bottle is working fine as urine may appear darker if a chin is dehydrated.
Some antibiotics may increase the levels of pigments in the urine.