I've bolded the incorrect part.
Find the number of order $3$ elements in $S_6$
My "Solution":
There are two ways to obtain these, either a 3-cycle or product of 2 disjoint 3-cycles.
Counting 3-cycles:
Choose 3 of 6 elements, this will determine the first 3 elements. We don't worry about the order of the rest. To get the distinct cycles (noting $(1 2 3) = (2 3 1)$), we fix the first element and permute the remaining elements. Thus: $\frac{6!}{3!3!} (3-1)!=40$
Counting Disjoint 3-cycles:
Choose 3 of 6 elements, this will determine the first 3 elements. Using the above computation we obtain $40$. We need to account for of the rest. Noting again that some cycles are similar, we fix the first element and permute the remaining to get distinct cycles, thus: $40\times (3-1)! = 80$
Thus: $120$ elements of order $3$.
The bolded reasoning is incorrect. The answer key says it should be 40. How am I over counting?
I like to think in terms of automorphism groups. That is, think of how many permutations of the symbols $1,\dots,6$ fix the permutation
$$ (123) = (123)(4)(5)(6). $$
So the question is: if we create a 3-cycle by taking a permutation of $6$ such as $312546$ and grouping together the first three elements to make $(312)$, how many times to we get the same 3-cycle?
With $(123)(4)(5)(6)$, we see that there are $3!$ ways to permute $4,5,6$ and they don't affect the 3-cycle we get. There are a further $3$ ways to permute $(123) = (231) = (312)$ without changing the 3-cycle. Thus there are
$$ \frac{6!}{3!3} = 40$$
3-cycles.
For products of two 3-cycles, we ask the same question but for the permutation
$$ (123)(456). $$
Again there are $3$ ways to permute $1,2,3$ and $3$ ways to permute $4,5,6$ without changing the permutation. But we can also exchange $1,2,3$ with $4,5,6$ to create $(456)(123)$. This gives us another factor of $2$ which you missed.
In total there are
$$ \frac{6!}{3\cdot 3 \cdot 2} = 40 $$
products of two disjoint 3-cycles.
With your solution, just note that you are counting $(123)(456)$ and $(456)(123)$ twice and divide by 2 to fix.