Is your menstrual cycle messed up if you stopped using the birth control pill and have missed a period but the pregnancy test came out negative?

Yes, there is a possibility you could still be pregnant. Some pregnancy tests will not read your hCG levels if they are too low. The best way to find out if you are pregnant after receiving a negative test result is to go to your doctor. Have your doctor perform a blood test to give you a definite answer as to if you are pregnant or not.