I don't think so. I had a separate passport from my mother's passport, which was issued about the same time as this 1968 Stanley Ann Soetoro application, and I was put on my mother passport application.
I think you are probably mistaken. As far as I know it is one passport per application. As a kid I was on one of my parents passports. Since the 1968 Dunham application is a renewal, it is not clear if Barack was on her passport or not. I guess we would have to find a 1965 passport application to see how it was worded.
It seems to me that Barack Jr. probably had a separate passport from his mother. Otherwise, she would have had to file for an amended passport to remove him when she wanted to travel alone. Of course it is possible that that is one of the missing applications.