Dont beleive anything the dealer tells you. I had this issue from day one and it took 7 trips to several dealers before finally solving the issue. NOT the drain tubes!!! Are these your issues??....right rear floor FLOODS until there is enough water in there to raise goldfish?? It will only do this when it pours rain for several hours, not after just a light shower or car wash?? If your Caliber is from the first year production, here is the solution!!!
Remove the right front fender...there you will find where the front firewall meets the cowl and doorjamb...this area is fit REALLY bad together!! The whole seam at that point needs to be caulked and sealed from the top to the bottom!! The reason it ends up in the rear floor??? I watched it, believe me, water rolls down through this area, into the kick panel, UNDER the front seat mount, through the front floor and ends up right in the back seat. The floorpan from the front to back seat has a long taper downward that sends the water flowing right to the back, but the reason it is this way is for the rear passenger legroom.
I struggled with the same issue for a LONG time....give that a try and I bet it is the same thing!!!