What Causes Delay In Periods?

Please, Help! I was 5 days for my menstruation. I always start on day 28 always. I had a tubal in 1999, however I felt like I was impregnate. I went to the ER due to pain in my left side that wrapped around to my lower stomach. I mentioned that my cycle was late and I wanted a urine preg test, before having an MRI. The urine came back negative and I had a pelvic exam and MRI. After the MRI and pelvic exam 2 hours passed and I passed a bright red clot which led to my cycle beginning what could this mean. If I was indeed pregnate would the MRI showed my pregnacy? Can the MRI show your tubes and if they have came undone would they have seen this? My cycle only lasted 3 days I normally bleed for 5 and spot 1 additional day