tleap was designed for linear sequences of residues like in protein molecules, so it auto-bonds each residue in the sequence it encounters them when reading a PDB file. For branched molecules, you must place a TER card between the residues that should not be bonded to each other (edit the PDB file and literally create a new line with the word "TER", between the residues), and then use the "bond" command in tleap to connect the correct residues to each other. E.g:
bond mol.9.C1 mol.7.O4
That creates a bond between the C1 of residue 9 and the O4 of residue 7. If you've made any mistakes, a good sign is that the charge will not be integral, i.e. it won't be -2.00000 but instead is -1.974.