In my fourier analysis script we learnt that the fourier series of a function $f\in L^1[0,1]$ must not converge to $f$ in $L^1$, i.e. in general we have
$||S_n(f)-f||_{L^1[0,1]}\not\to 0$.
$S_n(f)$ are the symmetrical partial sums of the fourier series. Later, the author says that for all $f\in L^1[0,1]$ we have for all $x\in [0,1]$ that
$\int_{0}^xf(y)dy=\lim_{n\to\infty}\int_{0}^{x}S_n(f) dy$.
Isn't this for $x=1$ a contradiction?
No, $\left|\int (f_n-f) dx\right|\to 0$ (the convergence you have) does not imply $\int |f_n-f|dx\to 0$ ($L^1$ convergence).