I added some cooked beets to a bread recipe. The result was a lovely pink dough:
After cooking, the rolls were yellow on the inside with some of the pink still visible in the crust:
Why? Any way to over come the color change?
It appears that the pH of your bread changed during baking. Beets are red because of their anthocyanins. According to Wikipedia:
Anthocyanins can be used as pH indicators because their color changes with pH; they are pink in acidic solutions (pH < 7), purple in neutral solutions (pH ~ 7), greenish-yellow in alkaline solutions (pH > 7), and colourless in very alkaline solutions, where the pigment is completely reduced.
You would have to post your recipe or analyze it yourself to determine what is alkalizing your dough, perhaps baking soda? Changing your recipe to make it more acidic may change the texture of your bread. You could look for another recipe that uses acidic ingredients, such as butter milk that might off set the color change. The pink looks very pretty though.
You will have to use food coloring if you want colored dough.
There are multiple problems with using fruit to color other food. First, the concentration is seldom high enough to get a noticeable color without using large amounts of the fruit, which would change the recipe texture if simply added. In this case, you were lucky to want the fruit there in the first place.
But the other problem is that these colors are not chemically stable. They can be destroyed by temperature, or by pH changes, as MiMintzer pointed out. But I wouldn't go messing with the pH of your dough. If you change it sufficiently to get the color to change, you will 1) change the leavening totally (probably get no leavening), and 2) change the taste a lot, so you end up with either sour bread or soap tasting bread. If what you are making is a yeast bread and not a quickbread, you'll still mess up with the yeast and therefore get bad leavening.
Beside the pH changes, you'll also get some change due to the different texture. The small amounts of dye sufficient to color a piece of solid dough will seem lighter after baking, when you're seeing a foam instead of a solid block. This won't account for the large difference in your pictures, but could contribute.
Bottom line: if you want pink bread, you have to color it with a real dye. Accidental colorations from berries are practically impossible to control.