Metal problem with fly wheel

I just built a motor and I did my first test with the motor out of the jet ski, every thing is good, but when I went to removed the fly wheel to put a little bit of grease at the bottom of the crank case under the fly wheel, I notice a few small piece of metals at the bottom of the case and when I look inside of the fly wheel I saw deep scratch on the magnet,

I just put the fly wheel back with out bolt and it is turning freely with no noise , I don't understand
 

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Your magnets may have picked up some debris prior to assembly, or you could of had something hiding in the bendix. Check everything carefully, ( bendix, coils, cover , flywheel), you may have more now.
 
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