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.

This blemish looks very much like a chemical spot, but it isn’t. It’s a location where a locating pin inadvertently pushed up the sheet metal. The sheet was peened back into place by the machinist, but the cold work altered the material enough to change the color of the anodizing.
This blemish looks very much like a chemical spot, but it isn’t. It’s a location where a locating pin inadvertently pushed up the sheet metal. The sheet was peened back into place by the machinist, but the cold work altered the material enough to change the color of the anodizing.

This dark spotting looks like something amiss in the anodizing tank, but it was actually caused by overly dirty water in a vibratory tumbler. The dirty media was embedded into the aluminum finish, causing blotchy areas.

Uncharacteristically, the welds on this bike frame caused little change in the anodizing color. However, poor sanding and left over spots of bondo create a surface finish that shows unanodized blotches and mechanical scratches.