Sub's cones are only made to move so far. You can over drive the cone excursion (so its called) by 1) overpowering it, either with too large of an amp, or an appropriate sized amp that is pushed into clipping... or by 2) running a signal well below the ported enclosure's tuning freq, with no subsonic filter for protection, or 3) simply by building too large of a box.
Figure out which one of those applies to you (probably clipping the amp) and correct the problem. Try making a more specific thread/question once you determine your actual problem.