Is this a metal bobbin or a plastic bobbin? In either case, over-filling can cause problems; there should be no thread past the edge of the bobbin top/bottom.
Plastic bobbins especially can distort if filled with too much thread. If it's a plastic bobbin, try taking off one-fifth to one-quarter of the thread.
Did you go at top speed to fill the bobbin? It is better to go at a moderate speed so the thread is not enticed to stretch on its way to the bobbin, then spring back once it is on (and add to pressure distorting the plastic bobbin).