One of the challenges as a GM of a decently sized group is being able to know how everyone will act with their characters. The largest issue I’ve seen with this comes from d20 games in which there is a Lawful/Chaotic and Good/Evil scale, or with characters who are inspired by similar “I’m X and Y” archetypes, because quite frankly I’ve never seen two people with the same definition for any alignment who haven’t exchanged notes beforehand.
First, it’s necessary to address the point of morality in a general context. Everyone has different morals. They’re related to our political beliefs and ideologies, but they’re also socially acquired based on our upbringings, and even in a society that is pretty uniform we still find that the background reasoning and arguments for and against certain moral actions can vary greatly. This is a major reason why it’s so hard to have reliable “good” characters at the table; some people may view the Inquisition of Warhammer 40k to be a “good” faction, especially considering the fact that its actions are typically justified by their results, while others might view it to be a “neutral” or “evil” faction just because it tends to be rough and violent in carrying out its aims.
As a GM, you want to get as good a feel for players’ characters as possible. Sometimes that comes in the form of telling them more about how a character in the setting would act; Legend of the Five Rings has a huge section on the etiquette, decorum, and ethics of high society in Rokugan, Likewise, it’s often appropriate for GM’s to tell players what the appropriate action for a situation is. Of course, this is not to conflict with a player’s privileges at the table, which include the freedom to undertake a reasonable action, but should be done rather than just punishing a player for a faux pas that they may not have meant to commit.
If you want to deal in more morally flexible characters, especially those who do things that aren’t appropriate or aligned to the setting, you’ll need to consider more than just a two-scale alignment. For this purpose I suggest having players take a personality test for their character; the Moral Foundations Questionnaire is one that I like on a casual basis, though most anything will get the player to consider consistent in-character actions and a moral code for their character. You could also have players draft an explicit list of proscriptions and prescriptions based on their convictions and beliefs, but I’ve found these to be of dubious value in play with emergent situations and they require a lot of effort-and tend to get amended in play or have situational conditions that become painful to keep track of.
Remember that the challenge in this, as it is in many things, is allowing your players freedom without stifling them, but as a GM you have a right to understand and know the characters in your game.