I've been searching and trying a few things for the last couple of hours and I can't figure out why there are yellow spots showing up on the normals when I bake them. Originally the wings had the same issue and the normals had to be flipped, but that doesn't seem to be working for the rest. Any ideas would be appreciated.
Baking normals can be tricky. If the normal of the lowpoly object is roughly the same as the highpoly object, the bake will be that bluish-cyan-pink that we like. However, if the normals points in opposite direction, the bake will be the inversion of those colors, as the yellow-brown-red.
Then why does the normals point in opposite direction? That could happen if the highpoly object intersects itself. The baking process have difficulty to find the correct face, with the correct normal.
Here are some images with a good and bad case:
In the second case the highpoly mesh intersects with itself. The lowpoly object can't be projected on the highpoly with a good result.