If there where heat spots and cracks on the flywheel and you didn't beat the crap out of it then you have been slipping your clutch too much and overheating it. They are probrably telling you this is from abuse and using that to deny coverage. Wrecking a clutch by slipping it too much will not harm the transmission IF it's not being subject to clutch dumps and similar forms of abuse, but if you are also shifting like crap which also usually goes along with clutch abuse then that could do it in too.