Hello friends, I have a 2009 Honda CRV. Is it

Hello friends, I have a 2009 Honda CRV. Is it normal for a vehicle to sometimes have a rough break-in period on a vehicle. I have had a lot had a lot of intermittent issues with this car, and have been told by some that it could just be the car breaking in. Some of my issues have been a bit of a rough downshift when I let off the accelerator. Sometimes the car shifts a little differently. Now when I drive the car for the first time of the day I hear a whining sound that seems to be coming from the engine, but it goes away after a couple minutes. Also the car will sometimes sputter under acceleration. I have taken it to the dealer once, and they pulled for codes and couldn't find anything. So I am thinking maybe just a rough break-in. Anyone have any other suggestions. Any input would be appreciated.