I'm making a 2-tier (9"/6") cake and using the SPS 6" plate with 4 pegs. The last time I made a stacked cake using SPS, when I pushed the plate with legs through the cake, it made the sides of the cake bulge out from the pressure from the legs. Do I need to take out the cake where the holes are gonna be? Or is there something I'm doing wrong/missing?

To me, it sounds like the legs were to short and and the weight of the upper cake slightly crushed the lower. Make sure all the legs are cut to the height of the bottom cake.

You may have also just push the plate and leg assembly in too fast. Go slow. Give the cake time to jam itself up into the legs. Also don't let the fondant or bc crust over before you put the SPS assembly into the cake.

And if those two things weren't the issue, then yes, your cake was too tall/the legs were too short.