Why are wire brushes bad?

I have seen many people mention not to use wire brushes to clean out their engines, why is this the case? Do they scratch the soft aluminum, or is there another reason?

It all depends on bristle metal, wire gauge and the metal being brushed. A special warning is in order to not use any kind of metal bristle on anodized surfaces-- i.e. the inside surface of the crankshaft bearing portion of a Bee crankcase.

I thought it was due to the tight tolerance that Cox was able to maintain during manufacturing that a “wire brush” cleaning of the cylinder could cause a loss of compression.
The best info I can find short term is from Paul G’s mouse racing info:

“Lastly, it is very important to keep carbon varnish off the piston and especially the cylinder walls. #000 steel wool or medium grade Scotchbrite wrapped around a small dowel wet with solvent easily removes all the carbon. This procedure takes only a minute, but really should be done before every contest to ensure peak performance. *NOTE: the Davis de- varnishing brush can also be used but be careful not to get carried away. Bob Davis recommends only a few strokes as his brush actually hones the cylinder. Used vigorously and too much can cause 'over-honing' making the piston fit too loose. Do be aware of this possibility.”