I didn't do Aero. Eng. at university, but I was in a similar situation. My BSc was in Astronomy, yet I never touched a telescope. My degree was all .... Maths. Sound familiar?
Now, strange as it may seem, that's been a blessing. I'm damn glad that I have that background now I am working in Astronomy at a professional level. At the time it was a pain in the backside, but there are subjects where you have to learn the basics. Sounds like Aeronautical Engineering is another one.
The mistake, it seems, is that the students come for the love of the subject (I did) while Universities are training people to have the skills they need to make a living working in the field. The two aren't necessarily the same thing.