You have left quite a bit out in your description – thickness, lay up, size, schedule. What temperature was the kiln at when you heard the break?
So I speculate. You heated up too fast for the the thickness of the glass. The first heating has a lot of separate pieces. The second firing is of a thicker single piece – go slower. Look at your manufacturer’s website and you will find a number of suggested firing schedules.
The brown mark is the binders of the fibre paper burning out. As you pass 400C – whatever that is in F – you will find that the stain has gone.
Kilns are robust. You will find it difficut to damage them, unless you drop them.
If you want you could go to the glass tips blog below and find a number of pieces of information that may help.