Fridge Brilliance: Rabbits can't count past four. It's beyond the scope of a rabbit's mind to do the kind of mental counting humans can do, so presumably they use their four paws.
This one could make Sliding Scale of Gender Inequality a feminist example of Level 1: if a bunch of does had chosen to leave an established warren, they probably wouldn't have gotten into nearly as much trouble, as does are the usual dispersers among rabbits and could easily dig themselves shelters as needed, while picking up a few solitary males along the way. It's because Hazel's group is bucks-only that their journey and their quest for mates run into enough near-disasters to rate as remarkable.
Presumably, the White Blindness is a disease carried by ear mites—not literally fleas, but certainly a small biting parasite that lives on a rabbit's ears. (And really, are rabbits likely to care much about the difference?)
It's myxomatosis, which actually is transmitted by being bitten by fleas or mosquitoes that have fed on an infected rabbit.
In the Sandleford warren, cowslips are considered to be a rare treat, to the point where some Jerkass Owsla bully Fiver away from one that he found just so they can eat it themselves. However, the cowslip plant is fairly toxic to rabbits. So when a rabbit who goes by the name Cowslip invites the protagonists over to his warren, it should be your first clue that something is very amiss with it.
Fridge Brilliance: The appearance of cars, cigarettes, and other modern artifacts in what feels like age-old folklore can seem incongruous, until you recall the very short lifespans of the storytellers. To a rabbit, there have been hrududil on the roads for countless generations.
Fridge Brilliance: The fact that the doe at the end is ostentatiously telling a story about El-ahrairah, but is actually telling Hazel, Fiver and the others story makes you wonder how many of El-ahrairah's stories actually are things he did, or if he ever really existed at all.
Or if he has existed thousands of times - a gestalt of every truly brave or ingenious Chief Rabbit.
All but explicitly called out in Cowslip's Warren. That warren has no chief rabbit because "A chief rabbit must be El-ahraira to his people and lead them from danger, but they have no danger except for one."