An ultra sound was conducted on my sister and at first, they said it was a cyst. today they are saying she's 3 months pregnant. how can this be?

Puzzling: I am not sure if they did another ultrasound(US) or when the first US was done. How much time between the US and the time they told you she was 3 months pregnant. So it is very difficult to answer your question. Sometimes it is not easy when the pregnancy is young but someone could have made a mistake. I would discuss with the people who did the US or her Dr. Hope this helped you.