They are probably just trying to be thorough so try not to stress. They do this whenever something comes up out of the ordinary. Due to an abnormal NT scan I had to have a scan to check on growth at 32 weeks and that then lead to another one to check the blood flow through the cord as that had come up as being on the high end of normal. In total I had 8 scans. Each time they suggested a problem i would worry myself sick and there was never ever a reason to do so.

When I had my NT scan I came in with a 1/37 chance of downs due to age and a 4.2 NT measurement. Amnio was suggested (as it's thought that it has 1/2 the m/c risk of CVS) and I did not hesitate in having one done. It was painless and I didn't get any cramping either. The lead up to the test and waiting for the results was the hard bit, not the procedure itself.

Like Kitt3n said the medical profession isn't even sure that CVS or amnio does increase the m/c risk. It could be that when women m/c after a procedure that they were going to miscarry anyway. There's no way of telling.

Try not to stress about it, more than likely all will be well when you get the NT test done.