How to know if computational calculations are correct
The only guaranteed way to achieve absolute correctness is to use asymptotically better methods and see the asymptotic behavior yourself. This, however, ofter requires prohibitively complex approaches.

Outside of that, one needs an experiment to check your data against. A good way (with limits) is to perform vibration frequency calculations and see if that fit the experiment. (making correction of unharmonic behavior). Another way is to run through similar well-studied cases and fit computational results. Most probably, a systematic error would be found, that can be easily eliminated. Luckily, most probably you are not the first to work with your particular kind of systems, so using google scholar it is usually possible to find a review or an establishing work that would list what work and what does not. Most practical methods have known 'glitches', and the ways to deal with them were considered. In particular, DFT cannot catch dispersion interactions, requiring empirical correction schemes.