What reasons could my lower stomach be nausea most of the day, and missed period but pregnancy test said negative when i took it?

Gyn issue: Your symptoms are likely gynecological and not gastro related. Should see your gyn.

Can retake HPT : in 7 days. Reasons for missed /late periods: low body weight, obesity, marked weight gain or loss, over-exercise such as in endurance athletes, breast-feeding, stress, illness, eating disorders (bulimia or anorexia), travel, hormone irregularities, drug use, medications (i.e., birth control) or med problem (polycystic ovary syndrome or Asherman’s syndrome. #1 reason is pregnancy.