look at where the binding is actually occurring; if the cleat isn't flush with the bottom of the sole then the sole needs to be relieved for sure but there could also be an issue with the cleat pocket being so narrow that the bindings er, bind against it.
In most current SPD pedals (even MTB double-sided ones) the intention is that part of the load is borne by platforms either side of the cleat. This only works if the cleat is flush with the sole of the shoe. If it isn't (with new cleats) then it is probably best if you take an angle grinder to the shoe sole; a local relief is all that is required but if you change to a different model of pedal (with different platforms) then a revision to this will probably be required.
cheers