There are several options here, the suitability of which will depend on the particular application. One option is to increase stencil thickness, either locally or across the whole stencil. However, this will affect the aspect ratio for printing and may lead to an increased chance of slump (bridging) in reflow. The stencil apertures may also be increased in size; when the solder melts it should pull back onto the pad and increase the joint volume.
If the volume of product is small, then using hand-soldering is a feasible option solder. Wire can be fed into an existing joint ensuring it is fully molten when doing so. Alternatively, the component may be added after the rest of the printed circuit board has been assembled, and the entire joint hand soldered.