The Affine Cipher is to encrypt a message $P$ to a cipher $C$ based on the following rule:
$$C\equiv aP + b \pmod {26}, \quad \gcd(a,M) = 1$$
Where the message is a combination of English alphabet.
The restriction $\gcd(a,M)$ is required to make the deciphering process achievable. If this restriction does not hold, the deciphering process will fail. Moreover, the enciphering process is not unique such that two message letters will be mapped to the same cipher letter.
Now, my inquiry is that, if $\gcd(a,M) > 1$, what is the cipher letter such that two message letters will map to?
My try:
My thoughts is to divide both the modulus $M$ and $a$ by the $\gcd(a,M)$. Then, the letter is $C - b$ will be mapped to two letters numbered $(00, a \times \frac{M}{\gcd(a,M)} \pmod M)$. Where $A:00, B:01, C:02 \cdots Z:25$. However, I cannot give a reason why. Is that true? Why?
Yes, your idea is essentially correct.
Let $d = \gcd(a, M)$. By definition, $a$ and $M$ are both divisible by $d$, i.e. $a = rd$ and $M = sd$ for some integers $r$ and $s$.
If $d > 1$, then $0 < s < M$, and so the numbers $P = 0$ and $P' = s = \frac Md$ represent distinct plaintext letters. But $$aP' = as = drs = rM \equiv 0 = aP \pmod M,$$ which implies that $aP' + b \equiv b = aP + b \pmod M$.
Of course, we can find other collisions, as well. In particular, any integer multiple of $s$ will also encrypt to the ciphertext $C = b$, since $ans + b = rnM + b \equiv b \pmod M$ for any integer $n$.
Also, for any integer $h$, the plaintext letters represented by $Q = h$ and $Q' = s+h$ also encrypt to the same ciphertext letter, since $$aQ + b = ah + b \equiv rM + ah + b = as + ah + b = aQ' + b \pmod M.$$
Of course, we can also combine these two results to show that $h$ and $ns + h$ will encrypt to the same value for any $n$ and $h$.