MOF-5 derivative structures contain excessively long bonds

[NanjeofKro]

When trying to generate MOF-5 analogues with different side chains, the resulting CIF files contain extremely long bonds (>20 Å) that traverse the unit cell and link atoms that should be bonded across unit cell edges. See attached CIF file (saved as .txt to allow uploading), generated by limiting the node selection to 6c_Zn_1_Ch and the edges to 1B_XYZ_Ch.
pcu_v1-6c_Zn_1_Ch_1-1B_4H_Ch.txt

[NanjeofKro]

Update: the same problem arises using other topologies, nodes, and linkers as well. I am working in Windows 10 Pro using Spyder through Anaconda, if that should be relevant.