Dear @Oisin ,
Covalent bonds are created based on the interatomic distances. Maybe the atoms are placed too far from each other? Could you please check the distance between atoms in your system - you can do it using the Measure editor by clicking on two atoms consecutively. Could you please attach a .cif file in which you experience the problem such that we could check it.
By the way, are you referring to .cif for biomolecules (mmcif/PDBx format) or .cif for crystals?