No, it did not show that vaccines caused miscarriage, it showed that some women who had the vaccines, also miscarried.
Correlation is not causation.
There are side effects to vaccines, absolutely, and that is something that I don't question at all. Do the possible, and known side effects outweigh the benefit, is the question that needs to be asked and studied.
I suspect that in some cases the benefits outweigh the detrimental side effects, and in some cases the opposite will be found to be true.
In the case of flu vaccines, I don't believe the risks are outweighed by the benefits, in the case of healthy people with no underlying health problems. This however, is just my personal preference and belief.