After doing a bit of carbon fibre skinning on my motorcycle I was pleased with the final result but after I washed the bike a few times it seemed to leave behind some water marks within it.
I sanded the part down again and then decided to lacquer it and that solved the problem but I didn't think I would have to do this?
I thought that once the resin had cured it would be water proof so I don't understand why it has done this, can anyone explain why this has happened.?

Very normal. Water can be quite harsh, even automotive paints will water mark quite easily due to the minerals that get left behind when the water evaporates. And especially if you used a soap and didn't wash that off fully, that can etch as well. This is why ceramic coatings and modern paint protection is so important, they make it a lot easier to keep your finish looking like new.

Also if it was relatively fresh as a part, if the epoxy isn't quite fully cured it is also more vulnerable to moisture absorption on the surface which in minor cases can cause a similar effect. 

I certainly agree some kind of wax or automotive type sealant is useful for long term protection from the elements and road grime on carbon parts.  Even basic automotive "wax" type products used on a semi regular basis will help.

Warren Penalver
Easy Composites / Carbon Mods - Technical Support Assistant