Whenever someone has a missed period, with or without other symptoms such as nausea, fatigue, or bloating, then pregnancy is always a possibility. This may have been what her doctor
meant when they met with your sister in law, that the possibility that she was pregnant was high. However, any suspicion of pregnancy needs to be confirmed with a formal pregnancy test, which can either be done on a blood sample or on a urine sample.
A blood pregnancy test is extremely sensitive, and it will generally be positive within 7 to 10 days after fertilization of the egg. Therefore, if your sister in law had a negative blood pregnancy test, it is very unlikely that she is pregnant, unless the test was performed in the narrow window of less than 7 to 10 days since fertilization. However, in this window of time, it would be unlikely to have any symptoms of pregnancy, and I assume that your sister in law went to the doctor for symptoms - in conclusion, I think very unlikely that she is pregnant!
Nevertheless, you should encourage her to follow up with her primary care doctor
about the symptoms. Her doctor may want to repeat a pregnancy test just to be sure and can also suggest other tests as needed.