That can happen at entire colleges as well.
For example, suppose student X is admitted as frosh to Highly Selective University but then barely makes it to graduation with a 2.1 college GPA. Meanwhile students Y and Z are not admitted as frosh and start at another college (perhaps a community college). Student Y earns a 4.0 and is admitted as a transfer to Highly Selective University and eventually graduates with a 4.0. Student Z earns a 3.5 and is not admitted as a transfer to Highly Selective University and eventually graduates from another college with a 3.5.
Getting back to selective majors, in general, unless the frosh direct admit students are subject to weed-out requirements that are similar to admission to major for those who enter undeclared or in another major, the situation where some frosh direct admits have GPAs lower than all of the secondary admits is not surprising.