Why do genital areas sometimes have an odor even when the person is clean?

Hygiene largely determines what odors you might encounter in this part of a body. How long has it been since she/he showered the area, using soap and water? A small amount of dried urine gives a similar odor to the genital areas of men and of women.

If you're not able to tolerate a little natural odor, make it a game to shower with partner before you get together. Keep in mind that the natural biochemical makeup of a woman's vagina will give it her own special fragrance, even after washing, but it will never be a rank odor unless she has an active infection.

Don't engage in sexual activites if either partner has an infection.

When urine is first excreted, it is virtually free of anything that we could consider infectious. After all, if this were not so our bladders and urethras would be infected. But urine does nourish bacteria after it is excreted. Check out Pasteur's swan-neck flask experiments. While urine is perfectly natural and often part of the natural scent of clean bodies, it isn't a good idea to think of urine as being 'sterile' for any length of time once it is outside of the body.