There were no such alpha issue, the example was 'broken'. Fixes #9 .

Examples/Tests/Layer.js

@@ -13,7 +13,7 @@ uniform sampler2D t2;
 void main () {
   vec4 c1 = texture2D(t1, uv);
   vec4 c2 = texture2D(t2, uv);
-  gl_FragColor = mix(c1, c2, c2.a);
+  gl_FragColor = vec4(mix(c1.rgb, c2.rgb, c2.a), 1.0);
 }
 `
   }