- Overcompleteness of basis functions
When a large number of basis functions is used for dense bulk systems with fcc, hcp, and bcc like structures, the basis set tends to be overcomplete. In such a case, you may observe erratic eigenvalues. To avoid the overcompleteness, a small number of optimized basis functions should be used. Another way to avoid the problem is to switch off the keyword 'scf.ProExpn.VNA' as

scf.ProExpn.VNA off # on|off, default = on

In this case, you may need to increase the cutoff energy for the numerical grid in real space by the keyword 'scf.energycutoff'. - Difficulty in getting the SCF convergence
For large-scale systems with a complex (non-collinear) magnetic structure, a metallic electric structure, or the mixture, it is quite difficult to get the SCF convergence. In such a case, one has to mix the charge density very slowly, indicating that the number of SCF steps to get the convergence becomes large unfortunately.

- Difficulty in getting the optimized structure
For weak interacting systems such as molecular systems, it is not easy to obtain a completely optimized structure, leading that the large number of iteration steps is required. Although the default value of criterion for geometrical optimization is Hartree/Bohr for the largest force, it would be a compromise to increase the criterion from to in such a case.