Wire brushes using steel wire can break off and embed into softer materials. If so, the wire will corrode (rust) and will appear in the softer material.
A more thorough method of cleaning, especially for subsequent coating for paint, is to use one of several "blasting" processes (sand, glass bead, walnut shell, vapor, etc.) or chemical dipping. A conversion chemical like POR can be used, but it's not heat resistant; better for non-heated parts.
Sherwood
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