Looking at the images in this article, I've noticed that the molecule electron density images showed as calculated via DFT look very symmetric, while those obtained by NC-AFM appear somewhat distorted. Namely, the ring at the left (the one with $\ce{OH}$ group) looks elongated, while the one at right is, on the contrary, compressed in horizontal direction, and the $\ce{OH}$ group seems to be tilted to the $\ce N$ atom. Also, the calculated image seems much more smeared, while the measured one gives some highly localized density "rods" for the bonds.
I've made a gif-combination of these two images so that the difference was easier to see:
Here the B is DFT-calculated version, while F is one measured by NC-AFM.
I can suppose one or several of the following might be among the reasons for this:
The substrate of $\ce{Cu(111)}$ wasn't taken into account when calculating(?), while in the measurement it appears to distort the molecule
DFT, being an approximate method, gives too simplified results
Smear vs thin rods difference might because in the DFT case the picture is of electron density while in AFM case the image shows AFM frequency shifts, which is not necessarily the same.
The probe of the microscope distorts the molecule
What are the true reasons for the differences?