Napoleon actually went to Brienne-le-Chateau, a Royal Military School, when he was 9 after learning French in only 4 months. At 15 he joined the École Royale Militaire which was also a military academy.

I can't answer if any difficulties came up with Generals or with public speaking, but Napoleon was famous for his speeches to his troops. They obviously quite easily understood him. I think the main problem with his French came from his spelling and grammar, which wasn't brilliant, although was less of a problem than nowadays because there was no standard French dictionary or rules.

This might be a good question for /r/linguistics .

French was not standardised as it is today, and many people would have spoken with a distinct regional accent or dialect.