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Over time yes it is bad.

It is decaying metal and you do not want that in your tank.
 

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Rust is basically Ferric Oxide (Iron which has broken down). If allowed to build up in enough quantity it can be toxic to fish.

If it is only a tiny amount of rust then scrapping it off probably would not hurt. A small amount will not cause any major problems but I would remove it all the same.
 
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