I've recently seen the example on how a shear $$\begin{bmatrix} 1 & 1\\ 0 & 1\end{bmatrix}$$ is an example of a defective matrix, since it has eigenvalues $1,1$ but only one independent eigenvector $\mathbf{v}_1 = (1,0)$.
So in this case, I can see that the algebraic multiplicity is greater than the geometric multiplicity, But what I am wondering is why the system created "two" eigenvalues when only one of them was "actually an eigenvalue" - (It's not even that there were two eigenvectors where each one corresponded $1$, $1$).
Is there any underlying reason why the system came up with two eigenvalues? (If I was to intuitively guess what would happen purely from a geometric perspective, I would have guessed that the characteristic polynomial would just be linear: $\lambda - 1$. Although this isn't possible for a $2 \times 2$, I was wondering whether there was any other meaning for the second eigenvalue?)
Well, I would say there is only one eigenvalue: $1$. The point is, we usually say it's "repeated" or that it has "(algebraic) multiplicity $2$". Think about what it means to "repeat" an eigenvalue; under which circumstances do we list it twice, or more? And, when we do, how many times should we be listing it?
You seem to be counting based on the dimension of the eigenspace for the eigenvalue (or equivalently, the maximum number of linearly independent eigenvectors you can come up with). This is known as the geometric multiplicity. And, indeed, the geometric multiplicity of $1$ is $1$ in this case. Note how it does not agree with the exponent of the $\lambda - 1$ factor in the characteristic polynomial.
The algebraic multiplicity counts the dimension of the generalised eigenspace. The generalised eigenspace is given by $$\operatorname{ker}(M - \lambda I)^n$$ where $M$ is an $n \times n$ matrix and $\lambda$ is an eigenvalue. Note how this contains $\operatorname{ker} (M - \lambda I)$ (if $(M - \lambda I)$ sends a vector to $0$, then applying it $n - 1$ more times will still send it to $0$), which is the (usual) eigenspace corresponding to $\lambda$. When $M$ is diagonalisable, this is invariably equal to $\operatorname{ker}(M - \lambda I)$, but when $M$ is defective, this can be larger than the eigenspace.
Now, as it turns out, the generalised eigenspaces always sum to $\Bbb{C}^n$, and as a consequence, we can always form a basis of generalised eigenvectors. There's a particularly nice class of such bases called Jordan bases; these are the next best things we can find to bases of eigenvectors. Instead of diagonalising a matrix, they turn it into Jordan Normal Form, an excellent consolation prize when a diagonal representation is denied to us. Jordan normal forms exist for every matrix, unlike diagonal forms!
The algebraic multiplicities also correspond to the exponents of the corresponding factors in the characteristic polynomials. In fact, some define the characteristic polynomial by this characteristic, and its determinant representation becomes a theorem.
In the case of the $2 \times 2$ matrix presented, the eigenspace, $\operatorname{ker} (M - I)$ is simply $\operatorname{span}\{(1, 0)\}$. However, if we compute $$\operatorname{ker} \left(\begin{bmatrix} 1 & 1 \\ 0 & 1 \end{bmatrix} - \begin{bmatrix} 1 & 0 \\ 0 & 1 \end{bmatrix}\right)^2 = \operatorname{ker} \begin{bmatrix} 0 & 1 \\ 0 & 0 \end{bmatrix}^2 = \operatorname{ker} \begin{bmatrix} 0 & 0 \\ 0 & 0 \end{bmatrix} = \Bbb{C}^2,$$ we see that the generalised eigenspace is $2$-dimensional, and the algebraic multiplicity is $2$.