As others have mentioned, it is pretty easy to distinguish the fancier fowlers from the period muskets by the engraving, type of barrel, carving, etc, etc. Where it gets sticky is in the more common or less expensive fowlers compared to the late 17th century muskets and even some of the Pre Land Pattern Brown Bess muskets for example. A lot of good info has already been brought up, but here's a little more.
1. I would suggest the most telling feature is whether or not it is made for use with a socket bayonet. Socket bayonets were pretty much standardized in Europen armies in the 1660's. If you have a rectangular stud instead of a front sight and the stock ends three to four inches form the muzzle, that's a darn good indicator of having been fitted with a socket bayonet and that pretty much rules out a civilian fowler. (However some fowlers here were retro fitted for bayonets and used as muskets and that get's confusing. Grin.)
2. Someone already mentioned most civilian locks weren't dated, but some musket locks in the early and late flint periods were also not dated. However, if there is an engraved crown on the lock of an English gun, that almost certainly means it was a musket because it denoted Crown property. American made contract muskets may have U.S. on the locks during the Rev War period.
3. Another quickly distinguishable feature would be whether or not there were military style sling swivels on the gun. I learned long ago to "never say never," but it would have been extremely rare to have seen military style sling swivels (especially the front sling swivel) on a fowler. These sling swivels were seen on Pre Land Pattern Brown Besses for example and some of them could otherwise be mistaken for fowlers by some people.
4. Where it really gets confusing is when you find military parts on what is most likely a fowler. These came from muskets that were considered too old or too damaged for repair and return as a musket. In England, outdated/unserviceable muskets were "broken up" and the brass parts usually melted down and recast in the current style. If the barrels could be reused, they were,but if not they would have been sold as scrap and some few of them found their way on civilian arms. If the locks were of an outdated style, they would also be sold and could wind up for use in East India or muskets purchased by civilian ship owners for example. Same thing would happen here in America. "Surplus" guns and parts in the hands of civilians goes back further than many of us think. Grin.
Gus