A remark and an alternative proof.
Remark: this problem as already been posed in the 1963 Putnam competition
https://mks.mff.cuni.cz/kalva/putnam/psoln/psol637.html
An alternative proof:
The arithmetical proof of @Ojas is perfect, but another one is possible.
I was in fact puzzled by the fact that when I solved (with the aid of Mathematica) the long division by $x^2-x+a$ ($a$ unknown), I obtained the same solution as you, @Ojas,without assuming integer (or rational) values for the coefficients; an afterthought said me that it is perfectly normal because long division with a single unknown coefficient gives (at most) a solution.
Then I thought that there should exist a non-arithmetical proof. Here is one.
Let $P(x)=x^{13}+x+90$; having an odd degree and being strictly increasing (its derivative is everywhere $>0$), $P$ has a unique real root. Thus its factorisation into irreducible factors in $\mathbb{R}[x]$ is a product of a first degree polynomial and 6 second degree polynomials, the latter having complex conjugate roots of $P$.
As a second degree factor $F(x)=x^2-x+a$ is imposed in the question, and because there is only one real root, this real root is a root of $Q(x)$. As the sum of the roots of $F$ is $1$, we have to look for conjugate roots of the form $\frac12 \pm bi$. There are such roots: $r_1, r_2=\frac12(1 \pm i\sqrt{7})$, whence $a=r_1r_2=\frac84=2$, proving the result.
Frankly speaking, I admit that $\frac12(1 \pm i\sqrt{7})$ is the rabbit pulled out of the hat...
By mere curiosity, I have represented on the same figure the roots $z_k$ of $P$ by blue dots and the roots of the "perturbated" polynomial $z^{13}+90$ i.e., $\zeta_k=re^{i(2k+1)\pi/13} \ (k \in \mathbb{Z})$ by black stars, with $r=\sqrt[13]{90}$. The two families are rather close. Roots $z_3$ and $z_{11}$ correspond to $r_1$ and $r_2$ and $z_7$ is the real root.
