Many of the unit discipline issues are the sort typical of just about any army — drunkenness on duty, sloppiness about gear maintenance, that sort of thing. Gaunther doesn't know enough about Blai's background to make the comparison explicitly, but compared to what Blai would have seen at his fort, there's somewhat more desertion; in most cases, it takes the form of Mendevian soldiers attempting to just go back home, and desertion in the heat of battle is actually rarer. There's significantly less interpersonal conflict than just about any Chelish fort, and some issues that Mendev essentially never has to deal with. The Queen in her mercy generally prefers to handle desertion outside the heat of battle (and that didn't involve defection to the demons) by sending the deserter to serve with the Condemned. It is possible desertion will be more of a concern than usual in the early days of the Crusade; the Queen wasn't sure how large of a force she'd need in Kenabres, and pulled some people away from their forts and (in the case of clerics) occasionally their villages to join the mobile force. ("Though I do expect it to stop being an issue once we've crossed the Wardstone barrier. Even cowards have enough sense not to run off into the middle of the Wound alone.")
In terms of morale, the Mendevian army wants reliable pay, enough to eat, frequent victories, decent weather, commanders who can act like they care about them, and the prospect of ever seeing their families. She also recommends against attempting to entirely prevent drinking or gambling or whoring, the way paladins are sometimes tempted to.
She needs an explanation of what the Lastwall handbook actually says, but when she hears it she purses her lips into a frown. "I expect this to be... controversial, Select. These rules may serve Lastwall well, but Mendev's needs are not the same as theirs."