My take, such as it is:
1. When flintlocks were the only system in use they were plagued by a lot of low quality cheaper locks and a lot of uneducated shooters who needed to shoot (soldiers and amateur hunters both rich and poor) so it’s easy to imagine how in non-expert hands with an inferior product, there was probably a lot of hangfires, flash in the pan, non-sparking, wet or lost prime, and other issues. Whereas nowadays the flintlock shooter is a dedicated enthusiast who is probably using an at least OK lock (the bad ones have all been weeded out of the fairly small market) and knows his business reasonably well, and can easily look up some best practices on the internet.
2. Percussion caps probably seemed notably more reliable and lots more weatherproof than a flintlock when they were introduced. Also way easier to train men on in a military setting. But nowadays they’re the more “entry level” muzzleloader so you get more casual hunter types and not the same percentage of hardcore enthusiasts as with the flintlock. Modern percussion caps can also be suspect since many are made explicitly for reenactment or blanks, and the percussion shooter is more likely to experiment with substitutes. Percussion guns are also more likely to have a patent breech which all things being equal should improve ignition efficiency a bit but doesn’t suffer fools in terms of cleanliness… you get a situation where several factors could well cause a misfire which makes it that much more likely that one, or a combination of them, will indeed do so.