I shouldn't be surprised. Become immersed in comparative religion classes, with a concentration on the academic evaluation of theological sources and it's easy to lose focus on the dogmatic truths taught by the infallible Sacred Magisterium.
The problem with such people is that in many cases there is no common ground for a true discussion of faith. A Catholic Apologist can discuss faith with a Lutheran, a Baptist or even a follower of Islam, but they cannot discuss faith with a secularist who denies the basic premises of faith. As Thomas Aquinas said in the Summa Theologiae :
If our opponent believes nothing of divine revelation, there is no longer any means of proving the articles of faith by reasoning, but only of answering his objections — if he has any — against faith.I told my young friend not to confuse the accumulation of facts necessary to pass his courses with the understanding of truths which can only be arrived at through the study of theologically sound doctrine. Proper catechesis prior to exposure is, like a vaccination, always better for spiritual health in such situations.