Because anodizing is a conversion coating, and relies on the aluminum substrate being converted to aluminum oxide, any defects in the aluminum will have marked effects on the quality of the anodizing. The basic rule to remember is that the aluminum finish must be consistent, clean and fully exposed for the anodic layer to form properly.
Common problems occur with welds, extrusions, cold or hot-worked areas, or poorly machined surfaces.
It is common for problems in the material or mechanical finish to have the appearance of a problem with the anodizing. Often material defects will look like chemical spotting or streaking, when the issue is material based. GIGO (garbage in, garbage out) is truer with anodizing than nearly any other finish. For the anodic layer to be perfect, the aluminum substrate has to be perfect as well.