For a simple check, just differentiate it and try to integrate. That should give you a satisfactory answer:
$$\int_{-1}^{1} \frac{\mathrm d}{\mathrm dx}\arctan\left(\tfrac{1}{x}\right)\,\mathrm dx = -\int_{-1}^{1} \frac{1}{1+x^2}\,\mathrm dx = -\frac{\pi}{2}$$
I think issue is as pointed in comments, the function $\arctan(\tfrac{1}{x})$ is not continuous over the chosen interval on integral, discontinuity at $x=0$. So you cannot apply fundamental theorem of calculus, but if you split the integral, then you can apply the theorem:
$$\int_{-1}^{1} \frac{\mathrm d}{\mathrm dx}\arctan\left(\tfrac{1}{x}\right)\,\mathrm dx = \int_{-1}^{0} \frac{\mathrm d}{\mathrm dx}\arctan\left(\tfrac{1}{x}\right)\,\mathrm dx + \int_{0}^{1} \frac{\mathrm d}{\mathrm dx}\arctan\left(\tfrac{1}{x}\right)\,\mathrm dx $$