Rotomolding is one of those processes where there is a little variation in each product. Unfortunately it's unavoidable, although I think Hobie has gone to great lengths to minimize it and holds several patents in the industry.
The Mirage Drive certainly stresses the drivewell, especially with Turbofins. the boats are engineered to handle this with an extra margin, but every once in awhile due to temperature, humidity, and other factors that cannot be absolutely controlled, this variation can cause something like a drivewell crack.
It is very hard to detect this type of problem until it actually happens. No doubt, that's why Hobie is so good with their boat replacement policy.
One of the biggest eye openers for me was getting to test a newly introduced foot powered prop drive last year in a rotomolded kayak from a different manufacturer. Attempting a simple sprint, their pedal unit literally ripped away from its attachment point on the second try. Whoops! This was something I do almost every day chasing boat wakes with the Hobie. I gained a huge respect for something I had always taken for granted.
Hobie provided additional reinforcement to the Adventure drivewell in mid '06 shortly after the Turbofins came out. As Yak says, the new '09 Click and Go Drive attachment system makes further improvements. Yet there will probably always be that odd boat that something doesn't come out right on. That's what warranties are for. As long as Hobie makes it good, I don't worry about it -- the boats are designed to be used!
PS Even if you're out of warranty, contact your dealer about options. As Yak also suggested, there are some excellent polyethylene bonding epoxies such as the 3M Scotchweld DP 8010 and Loctite 3030.