I find it hard to believe that anyone reading this doesn't know this but: The DM is always right or more correctly: The DM has power over the rules. There is a 1B to this. The DM MUST be consistent in this and tread lightly.
It is important when using this rule to have a consistent pattern to it. If you are going for a more realistic approach to gaming (something I disagree with), you should enforce this across the board. If fact you are better off with coherent house rules than constant DM fiat. If you are going to take a loose approach to the rules, make sure the players get this benefit too.
A note on monsters and NPCs.: You never need to justify powers and abilities of these UNLESS you are operating a DM NPC (which must be used with care anyway). I advise only experienced DMs go the DM NPC route, and you are always better off letting the PCs have limited control over their NPC companions to a greater degree to avoid DM bias. If you want a DM NPC you should prob find a game and play in it instead. I have used DM NPCs in the past and will no doubt use them again but keep their power in line w/ the PCs(maybe a L or 2 lower)
Individual monster types can always break the rules, but again be consistent. It should be reserved for boss monsters and not Orcs. Making a Liche have triple the number of HP is fine, be challenging not killer.