I had exactly the same thing and went for a whole heap of check-ups because I was so concerned. My OB said that it is very common because our poor heart has to pump so many extra litres of blood around our body / to our baby when we are pregnant. So basically it is just working extra hard and that is why we notice it (rapid beating, flutters and shortness of breath).

Regardless, though, I would be getting it checked out either way. In my opinion it is just not worth taking chances when it comes to any of one's vital organs.