It was shown by Boukerrou et al.~[IACR Trans. Symmetric Cryptol. 1 (2020), 331--362] that the $F$-boomerang uniformity (which is the same as the second-order zero differential uniformity in even characteristic) of perfect nonlinear functions is~$0$ on $\F_{p^n}$ ($p$ prime) and the one of almost perfect nonlinear functions on $\F_{2^n}$ is~$0$. It is natural to inquire what happens with APN or other low differential uniform functions in even and odd characteristics. Here, we explicitly determine the second-order zero differential spectra of several maps with low differential uniformity. In particular, we compute the second-order zero differential spectra for some almost perfect nonlinear (APN) functions over finite fields of odd characteristic, pushing further the study started in Boukerrou et al. and continued in Li et al.~[Cryptogr. Commun. 14.3 (2022), 653--662], and it turns out that our considered functions also have low second-order zero differential uniformity. Moreover, we study the second-order zero differential spectra of certain functions with low differential uniformity over finite fields of even characteristic. We connect this new concept to the sum-freedom and vanishing flats concepts and find some counts for the number of vanishing flats via our methods. We provide detailed analyses on several equations over finite fields that may have an interest outside of the scope of our paper.