No this is issues with the palette sometimes very hard to avoid. So what happens is if there is a wide variety of colours that need to fit into 256 colours. So some of the blacks have been replaced to use RGB 0,0,0 which is ment to be the bit underneath the studs. RGB 0,0,0 is ment to be transparent but if the palette assigns this to any other pixels then you end up with the Spikes and sometimes a black tongue on some boots(i think only visible in the in-game editor)
What you would have to do is start again and force lots of blacks, sacrificing some of the colours, the boots wouldnt look so good. So a good solution would be to have less varied colours. Hopefully konami will have a bigger palette, and make it so you have two boot images one for the left boot and one for the right.