Is there a continuous function $f : ]1, \infty[ \to \Bbb R_{>0}$ such that $f(x) \to 0$ when $x \to +\infty$ but $$\lim_{x \to +\infty} \dfrac 1 x \int_1^x f \;\neq\; 0$$ (either the limit doesn't exist but a better example for me would be when it exists and is $>0$)?
I tried something like $f(t) = \dfrac 1 {\log\big(\log(t)\big)}$ but I'm not sure how to handle the integral. The problem seems to be when $f$ doesn't go to $0$ sufficient quickly.
No.
If $f(x)\to 0$, then you can find an $x_0$ such that $f(x)<\varepsilon/2$ everywhere to the right of $x_0$, and then no matter how large $\int_1^{x_0} f(t)\,dt$ is, you can always push $\frac1x \int_1^x f(t)\,dt$ below $\varepsilon$ by choosing $x$ far enough to the right of $x_0$.
Of course you do need to assume that, say, $\int_1^2 f(t)\,dt$ exists (and is finite) at all. For example, if $f(t)=\frac{1}{t-1}$, then $\frac1x\int_1^xf(t)\,dt$ never exists (or is always infinite, depending on your conventions).