Aligners are made from a digital impression so that they fit the teeth snugly, which is important for the treatment to work. Any change to the shape of a tooth, such as a new filling, can stop the aligners fitting properly and affect the planned tooth movements.
If an emergency arises – for example, a piece of tooth breaks off – and a new filling is needed, it can be made smaller so that it does not interfere with the aligners. Another option is to place a temporary filling, which is later replaced with a permanent one before the next planned rescan of the teeth.
This answer is for general information. Your own case needs an examination by an orthodontist.