That's typical on any weld, with the exception of really high end work you just aren't going to find anyplace in the auto industry.
Basically with a weld you take metal, similar to what you are welding, add heat, and melt it all together.
The metal that is being added is typically of a lower quality than the actual part and the process of melting the metals burns alloys off (alloys are other metals added to make metals that don't rust).
Anyway I think what you've got is commonly referred to as "surface rust". Typical on any non exotic metal that has exposure to the outside.
Jon