Yes. The Charleville was .69 calibre, whilst the Brown Bess was .71
A miniscule difference, but enough to render the former unable to use the latter's cartridges.
As to which weapon I view as better;
I have to go with the Charleville, despite the ammunition issues, simply because it would be easier to maintain, and would be less likely to fall apart when you beat someone over the head with it. (Pinned vs. Banded barrel)