What could be happening

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Okay ladies so my cycle was due on the 16 on one app it says 3 days late(flo) and on this app it said 5. I went to the emergency room. Pregnancy test came back positive after being faint over the last two days but they couldnt see anything on the ultrasound according to my doctor notes. They did say I have a corpus luteum cyst which came days after I started bleeding off and on. What could be the cause of this could I be pregnant I would've only measure 3-4 weeks.