What Causes Delayed Periods With Negative UPT?

I went off the pill 2 months ago. Got a heavy period last month. This month I m 2 days late. Have an ovarian cyst on my right ovary 4.8cm. And thickened endometrium. Did 2 home pregnancy tests and they were negative. Had safe sex using a condom. Am I pregnant or is my body trying to regulate?