I am looking at a probability breakdown of lowball hands (lowest $5$ distinct cards, $12345$ being the best) here: http://www.durangobill.com/LowballPoker/Lowball_Poker_7_cards.html
The website lists the total number of $5$ high hands as $781,824$. Using a standard deck, I thought that the counting methodology would be $(4C_1)^5 \cdot (47C_2)$. This overestimates the amount of hands however. Why is this not the correct way to count?
You're double (and triple, and quadruple) counting because sometimes one or both of the $2$ cards you choose out of $47$ are lower than a 6.
For example, the hand consisting of Ace through 5 of diamonds and the Ace and 2 of hearts is counted 4 times.
The hand consisting of Ace through 5 of spades plus both red Aces is counted 3 times.
The hand consisting of 2 black Aces and the 2 through 6 of hearts is counted twice.
To set this up right, let's partition the cards: 20 cards are less than 6, 32 cards are 6 or more.
First let's count all the hands we don't need to double count or half count:
$${4 \choose 1}^5{32\choose2}$$
Next let's tackle the hands with 2 of some value below 6 (the value to be doubled is chosen out of five possible values):
$${5\choose1}{4\choose2}{4\choose1}^4{32\choose1}$$
Now let's tackle the hands with 3 of some value below 6 (note the 32 choose 0 included for completeness):
$${5\choose1}{4\choose3}{4\choose1}^4{32\choose0}$$
Now let's tackle the hands with 2 distinct values below 6 for which there are 2 cards:
$${5\choose2}{4\choose2}^2{4\choose1}^3{32\choose0}$$
Adding these figures together, we get 781824, just as stated on the page you linked.