Once you look at enough varied pictures of different venomous species you are able to tell the difference quite quickly. I'm lucky that I've had enough time on my hands over the years to sit and browse hundreds upon hundreds of google images of different species, comparing the different regional variations and colour differences.
From an evolutionary perspective, cottonmouths and pygmy rattlers are more alike than you might think. Not only because they tend to occupy the same (ish) region of the world - with similar threats and temperatures etc etc... so the physical adaptations they have made to live in their respective environment/s are fairly similar - hence it is no surprise that they might look similar too.
By comparison: there is no mistaking a desert snake from a jungle snake, for example.
These two species of snakes we are talking about here are distantly related... there is no doubt about that. At some point in time, maybe hundreds of thousands of years ago, they may have been one and the same species which split off a single genetic line.
You can barely hear a pygmy rattlesnakes rattle... because it is so small. Sometimes it is almost impossible to hear. So poking it with a stick to see if it rattled might not be a great option. Just FYI.