Not a complete answer,
$$I=\int _0^1\frac{\log^2 \left(x\right)\operatorname{Li}_2\left(x\right)}{1+x}\:dx$$
Using the Cauchy product,
$$\log(1-x) \, \text{Li}_3(x) = \sum_{n=1}^\infty x^n \left( 4 \frac{1}{n^4} - 2 \frac{H_n}{n^3} - \frac{H_n^{(2)}}{n^2} - \frac{H_n^{(3)}}{n} \right)$$
Using,
$$ \boxed{\operatorname{Li}_4(x)=\sum_{k=1}^\infty\frac{x^k}{k^4}} $$
$$\log(1-x) \, \text{Li}_3(x) = 4\operatorname{Li}_4(x)-\sum_{n=1}^\infty x^n \left( 2 \frac{H_n}{n^3} + \frac{H_n^{(2)}}{n^2} + \frac{H_n^{(3)}}{n} \right)$$
$$I=\int _0^1 \frac{1}{1+x}\left[\color{red}{4\operatorname{Li}_4(x)}-\sum_{n=1}^\infty x^n \left( \color{blue}{2 \frac{H_n}{n^3}} + \color{green}{\frac{H_n^{(2)}}{n^2}} + \color{brown}{\frac{H_n^{(3)}}{n}} \right)\right]\,dx$$
$$I=\color{red}{4\int_0^1\frac{\operatorname{Li}_4(x)}{1+x}\,dx}-\left[\sum_{n=1}^\infty \left( \color{blue}{2 \frac{H_n}{n^3}} + \color{green}{\frac{H_n^{(2)}}{n^2}} + \color{brown}{\frac{H_n^{(3)}}{n}} \right)\right]\int _0^1 \frac{x^n}{1+x}\,dx$$
We have,
$$\color{red}{4\int_0^1\frac{\operatorname{Li}_{4}(x)}{1+x}\mathrm{d}x=4\ln(2)\zeta(4)+3\zeta(2)\zeta(3)-\frac{59}{8}\zeta(5)}$$
We have,
$$\int_0^1 \frac{x^n}{1+x} {\rm d} x= \frac{1}{2} \left[ \psi \left( \frac{n}{2} + 1\right) - \psi \left( \frac{n}{2} + \frac{1}{2} \right) \right]$$
Or we have the alternate,
$$\int_0^1 \frac{x^n}{1+x} \, dx = \frac{1}{2} \left( H_{\frac{n}{2}} - H_{\frac{n-1}{2}} \right)$$
Now comes the challenging part of computing,
$$S_1=\color{blue}{\sum_{n=1}^\infty\frac{H_n}{n^3}\psi \left( \frac{n}{2} + 1\right)}$$
$$S_2=\color{blue}{\sum_{n=1}^\infty\frac{H_n}{n^3}\psi \left( \frac{n}{2} + \frac{1}{2} \right) }$$
$$S_3=\color{green}{\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^2}\psi \left( \frac{n}{2} + 1\right)}$$
$$S_4=\color{green}{\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^2}\psi \left( \frac{n}{2} + \frac{1}{2} \right) }$$
$$S_5=\color{brown}{\sum_{n=1}^\infty\frac{H_n^{(3)}}{n}\psi \left( \frac{n}{2} + 1\right)}$$
$$S_6=\color{brown}{\sum_{n=1}^\infty\frac{H_n^{(3)}}{n}\psi \left( \frac{n}{2} + \frac{1}{2} \right) }$$
Reference :
$$\psi\left(n+\frac{1}{2}\right)=2H_{2n}-H_n-\gamma-2\log(2)$$
$$H_n = ψ(n + 1) + γ$$
We do a nice form for the alternate,
$$I=\int _0^1\frac{\log \left(1-x\right)\operatorname{Li}_3\left(x\right)}{x}\:dx$$
$$\frac{\log(1-x) \, \text{Li}_3(x)}{x} = \sum_{n=1}^\infty x^{n-1} \left( 4 \frac{1}{n^4} - 2 \frac{H_n}{n^3} - \frac{H_n^{(2)}}{n^2} - \frac{H_n^{(3)}}{n} \right)$$
$$\int_0^1 \frac{\log(1-x) \, \text{Li}_3(x)}{x}\,dx = \sum_{n=1}^\infty \left( 4 \frac{1}{n^4} - 2 \frac{H_n}{n^3} - \frac{H_n^{(2)}}{n^2} - \frac{H_n^{(3)}}{n} \right)\int_0^1x^{n-1} \,dx$$
$$\int_0^1 \frac{\log(1-x) \, \text{Li}_3(x)}{x}\,dx = \sum_{n=1}^\infty \left( 4 \frac{1}{n^5} - 2 \frac{H_n}{n^4} - \frac{H_n^{(2)}}{n^3} - \frac{H_n^{(3)}}{n^2} \right)$$
$$\int_0^1 \frac{\log(1-x) \, \text{Li}_3(x)}{x}\,dx = 4\zeta(5)-2\color{green}{\sum_{n=1}^\infty \frac{H_n}{n^4}} - \color{red}{\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^3}} - \color{blue}{\sum_{n=1}^\infty\frac{H_n^{(3)}}{n^2}} $$
From here,
$$\color{red}{\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^3}=3\zeta(2)\zeta(3)-\frac92\zeta(5)}$$
$$\color{blue}{\sum_{n=1}^\infty\frac{H_n^{(3)}}{n^2}=\frac{11}{2}\zeta(5)-2\zeta(2)\zeta(3)}$$
From here,
$$\color{green}{\sum_{n=1}^\infty \frac{H_n}{n^4}=3\zeta(5)-\zeta(2)\zeta(3)}$$
$$\boxed{\int _0^1\frac{\log \left(1-x\right)\operatorname{Li}_3\left(x\right)}{x}\:dx=\zeta(2)\zeta(3)-3\zeta(5)}$$
Reference :
$$\color{red}{\int_0^1 \frac{\log(x)\operatorname{Li}_2(x)}{1-ax}\,dx=\frac{(\operatorname{Li}_2(a))^2}{2a}-2\zeta(2)\frac{\operatorname{Li}_2(a)}{a}+\frac{3\operatorname{Li}_4(a)}{a}}$$
From David H's comment,
Here's an idea,
$$\int_0^1 \frac{\log^2(x)}{1 + x}\mathrm{Li}_2(x) \, dx = \frac32\zeta(2) \zeta(3) - \int_0^1 \frac{\log^2(x)}{1 + x} \sum_{n=1}^\infty \frac{1 - x^n}{n^2} dx$$
$${\because\int_{0}^{1}\frac{(\log(x))^nx^{p-1}}{1+x^q}dx=\frac{1}{q^{n+1}}\beta^{(n)}\left(\frac{p}{q}\right)\implies\int_{0}^{1}\frac{(\log(x))^2}{1+x}dx=\beta^{(2)}\left(1\right)=\frac32\zeta(3)}$$