This article deals with the issue of perforating point defects (pores) in a bilayer heterostructure composed of striped borophene and graphene. Three types of non-equivalent vacancies of the minimum size are considered. These include a single vacancy and two double vacancies. The study of the properties and stability of the perforating defects in borophene-graphene heterostructures is important given the increasing role of such structures in membranes for water purification, renewable energy generation, and other osmotic applications. Using the DFT method, the atomic configurations and main energy characteristics of the proposed defects are obtained. The results show that the formation of a single boron vacancy on the borophene side of borophene-graphene requires less energy than the formation of a carbon vacancy in graphene. Comparisons between double vacancies in nanoscale materials are unreliable because different reference systems produce the different chemical potentials. The problem of choosing the reference system for reliable calculation of the vacancy formation energies is posed and discussed. Using borophene-graphene as an example, it is shown that the reference system strongly affects the magnitude and sign of the vacancy formation energy. Hydrogenation is tested to stabilize the proposed defects.