I was doing some reading on Trample and in the Bestiary its listed as doing the creatures Slam damage plus 1.5 STR. But on the Elephant and Mastodon both list the damage as a die class higher than the slam.
The specific entries in the creatures' statblocks trump the general rules for determining such things.
If you thumb through the Bestiary you'll find quite a few critters that bend the rules in one way or another. Having different damage dice is the most common.