Pregnant after IF

Really late ovulation after trigger shots??

Can anyone give me some advice?
I have severe pcos and struggled to conceive for almost 3 years with my first child. 
I got pregnant naturally and unplanned last August but had a miscarriage at 10 weeks. It went wrong and I hemorrhaged and almost lost my life.
We decided to start trying again this January with the doctor's supervision using letrozole, duphaston and trigger shots. 
I got a bfp and went for a scan at what I thought was 6 weeks 3 days. However, the doctor could only see the pregnancy sac and no foetus and I was measuring at 5 weeks 3 days!
I'm freaking out because I don't see how this is possible considering we had trigger shots to pinpoint ovulation. 
I have another scan on 9th but my mind is going crazy. 
Has anyone else had an experience with late ovulation after trigger shots? Like way over 72 hours or is it more likely that I'm going to miscarry again? 
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