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Depends on where it's broken. If it's near a mounting bolt, my guess it was over tightened by your clutch installer. If it's broken elsewhere, my guess it resulted from a manufacturing defect. I don't see anyother reason, even abuse of the car (not pointing fingers, here) should not break the bellhousing, unless if came from within from the original clutch generading? Good luck.
They are not sure why it broke.
The car chattered so bad that they think the flexing of the input shaft may have caused this to happen.
Just looking to see if this has happened to any one else.
"Flexing of the input shaft"? Let's see, where/how would it flex? Side to side? Up and down? In or out? I don't think so, not with the end of the input shaft seated into the thrust bearing in the crankshaft. I'd say it wasn't lined up or fully seated evenly and one or more bolts tightened up too much and it cracked.
I whole heartedly agree with Hawk - my opinion - the installed used the bellhousing to "pull in" the trans input shaft. I have seen shops do this with longer trans bolts.
Find out where the crack is.
I had the Spec III+ installed at the dealership, the mechanic told me the same thing in regards to chattering insofar as it should decrease with some miles. I have found this to be true however it still chatters usually in reverse or in 1st gear. The III+ clutch according to the vendor has two extra 'pucks' to alleviate the chattering.
I'd bet my paycheck they broke it and want you to pay for their screw up. I've had the motor apart a dozen times, its easy to do during install. Its not going to break unless a clutch explodes.