Strange artifacts on Vertex Color Shader

I am using Vertex Color shader for coloring my generated mesh. I have a problem, when I want to reduce alpha of mesh color, e.g. for water, I get strange artifacts on the mesh.

Here is shot without water having any alpha:

• http://i.imgur.com/1Bmjpio.png

Here is shot with water mesh having reduced alpha - problem is seen here

• http://i.imgur.com/QKBGxGR.png

Here is one shot under water, no faces / polygons are sideways that could cause the problem

• http://i.imgur.com/J5poco7.png

Here is wireframe mode

• http://i.imgur.com/6zJOrRb.png

The problem is in 2nd picture, water having artifacts with alpha reduced. The color changes depending on Camera Background color, e.g. red-ish in this example.

Shader I use:

 Shader "Custom/Vertex Lit - Shadows" {
     SubShader{
         Tags{ "RenderType" = "Transparent" "Queue" = "Transparent" }
         Blend SrcAlpha OneMinusSrcAlpha
 
         CGPROGRAM
         #pragma surface surf Lambert keepalpha fullforwardshadows
         
         struct Input {
             fixed4 color : COLOR;
         };
         void surf(Input IN, inout SurfaceOutput o) {
             o.Albedo = IN.color.rgb;
             o.Alpha = IN.color.a;
         }
         ENDCG
         }
         Fallback "VertexLit"
 }