That sounds like the setting. You would be using less pixels with the 3:2 aspect ratio.
Since you said you had cropped the photos prior to sending them to the printer, you could have cropped them to a 3x2 ratio. I do that often.
I use Adobe Photoshop Elements and when you use the selection tool, you have the option of setting the aspect ratio to 3:2 or anything. Then every selection rectangle will be 3:2 and you only have to decide how large to make the rectangle and where to put it.
Then when you do the crop, you get a perfect 3:2 ratio photo.
Just obtained our first digital camera recently, uploaded pictures to computer, cropped them to the way we wanted them to look as a finished product, and had them printed at Costco. Well, the printed photo's had the top of people's heads cut off lol. The helpful person there indicated that since we were printing 4x6 prints, there should be a setting on the camera itself to change the aspect ratio to 3:2 which would make the printed product look like the edited photo. I found in the menu setting, "picture size", and if I change the megapixels to 4.4 instead of 5.0, there is a [3:2] indication by it. Is this changing the aspect ratio as well as lowering the megapixels? Thanks for any help.