Aggression in the pregnant mare could be due to a number of factors, including hormonal changes or discomfort. However, the main possibility that needs to be eliminated is something called a granulosa thecal cell tumour (GTC). GTC is a steroid producing tumour, which will generally produce testosterone (the male sex hormone) and cause your mare to behave as if she were a stallion.
GTCs are relatively easy to find on an ultrasound scan, and can be confirmed with blood tests for testosterone and inhibin.
It is best to consult your stud vet, ask their advice and get them to perform an ultrasound scan if appropriate.