The first hybrids that came out were not designed the way they are now.
Bunk doors didn't close right allowing water in.  Especially the front bunk when towing.
I haven't heard of any hybrids built in the last few years with any water issues (bunk related).

We bought our hybrid new in April.
A good rain came through and later in the day I went outside to show my brother our new hybrid..... With water on the floor.

Had nothing to do with being a hybrid.  A part in the furnace was broken allowing water to come in through the furnace exhaust. 

In our case, it was definitely poor installation.

On our 2011 Palomino HTT that we sold two months ago, I had some issues with my front bunk leaking at one point.  One day, I opened up the front bunk to find a small puddle sitting in the middle of the folds of the vinyl top.  Fortunately, it hadn't seeped through the vinyl top or run anywhere else, and no water got otherwise inside as far as I could tell.

The bunk doors on our unit had two seals, the outer seal was attached to the edge of the bunk door and mated up with the outermost edge of the door frame.  The seal is the black gasket runs around the outer edge of the door in the pic below.

The inner seal was attached to the door frame and contacted the the inner-most part of the metal on the door.  You can see the white gasket in the picture below.

It is supposed to mate up with the white metal part on the door that's facing up and right next to the faux wood.  Note that the pic of the door above is with the canvas almost entirely set up, with just the corner pulled back to take the picture, which is why you see so little of the seal and metal.

These pics are of the rear bunk, but all three bunk doors were essentially the same, just the front one was a slightly different size.  The observant among you may notice that in the second picture, there's a line across the top left by the outer seal where it contacts the door frame.  It runs right across the screws, which means the seal doesn't have good contact with door frame in those spots.  As I'm sure you can imagine that any water wanting to to get in is going to find those gaps.  I ultimately wound up installing a second row of seal tape just inside the first outer seal.  The second row would contact the door frame just inside the row of screws and get a good seal because it was mated up with flat metal.  Between the two rows, it kept the water out until we sold it.

I'm not certain the white inner seals actually made contact with the door like they were supposed to, otherwise, I shouldn't have found that puddle.  I was never able to confirm it, since it would have required disconnecting the tent material from the door to get my head in there while the door was closed, and I never had a reason to pursuer it further after installing the additional outer seal.

Our trailer had the lever style latches on the doors.

I think those are the ones that are supposed to be better and the ones that are like a gigantic wingnut are supposed to be one of the styles with problems.

I have a Jayco 2010 17C and yes my bunkends did leak. The rear was the biggest problem and caused most of the damage. The biggest issue is make sure nothing is traped between the door and the seal. A small leaf will cause a big leak. In a way this was a blessing. jayco does not put peep holes in areas that need to be checked for water, like right below the front and rear bunkends. After taking out all the water damage I put in lift up panels in the rear and front. The rear bunk was always cold. We could never get enough heat back there without over heating the front of the camper. After removing the water damaged board (Fake Wood) that covered the rear bunkend I found the heater duct completely crushed. The sewer tube was not fastened or sealed, glade it was never used. In the front there is a lot of wasted space. The fiberglass bat was just thrown in there. I now do not close my bunkends with the bed cushions installed. This has helped in double checking to make sure the canvas is not pinched and the seal is tight. I haven't had a leak in either door since and the removable panels I put in the front and rear allow to use that wasted space for storage and to check for water leaks.