2010 Mazda 3 I Intermittent 2nd Gear Grind

I'm new and and don't know much about cars, and looking for a little bit of advice. I just purchased a used manual car with 30k miles. It has a 1 year bumper to bumper and 100k power train warranty. After I purchased it, every so often when trying to shift from 1st to 2nd it wouldn't go into gear and have a loud grinding noise. At first I thought it could just be some poor driving on my part, but I have been driving manual for a few years now. I made sure that my clutch was fully depressed when this was happening. This was happening anywhere from 2K rpms and up, so I wasn't redlining it or anything. I did a lot of research and talk to a lot of my car buddies. Everything is pointing to a synchro problem. I took it into the dealership just now and instantly they're telling me its a clutch issue, which I know is not cover under warranty. I knew the clutch did need replacing when I first drove it. This is why my salesman cut me a "deal" with $300 off the car price for that issue. I guess my question is, could it really be a clutch issue? If I go back and they're telling me this, I would just like to be as well informed as possible so I don't get taken advantage of. Thanks for any advice in advance.