BCM was replaced

My truck was taken to the shop to have the flex plate
replaced. As a result they said my body control module
malfunction. I was surprised to have a bill for replacing the
BCM also. They say it is common for the body control
module to malfunction After the torque converter is
disconnected. I picked up my truck today and it was
running horribly and the check engine light came on. I had a
scan ran on it and it came back as a crankshaft position
sensor malfunction PO336.The mechanic told me that this
has probably been going bad because he found several
codes on my truck several months ago. Mine you, when I
brought the truck in there were no check engine lights or
any other warning lights. Please tell me if this is common. I
feel as if they may have missed up something when
changing out the flex plea and is now trying to run up a bill
on me to fix whatever they caused.I think that they may
have missed up something when replacing my fly wheel.
When I brought the truck in there were no lights on what so
ever. The only problem I had was a tapping noise coming
from what I assume to be the flex plate that needed to be
replaced.