I don't think it's necessarily a problem. At the graduate level, you're expected to learn things in many other ways besides formal courses: self-study, informal seminars, independent or supervised research, individual discussions with faculty or other students, thesis work, etc. Likewise, you'll have evidence of your learning in other forms besides course grades: published papers, your thesis (if it's a thesis-based program), recommendation letters from supervisors, etc.
So this isn't necessarily a red flag. However, it is worth bringing it up with prospective advisors or others in the program: "I want to work in NLP. What opportunities exist for building skills and doing research in this area?"
One note is that besides being accepted to the program, if you want to work in a particular research group, the faculty leader(s) of that group will have to agree. And there could be obstacles unrelated to your abilities - too many students in the group already, not enough funding, etc. So if you are really tied to working in this particular area, then before deciding to attend the program, you should talk to the group(s) that work in your area of interest, and find out if it is feasible for you to work with them.