Charming a creature gives you a +50 reputation bonus in its eyes. Reputation runs from 0 to 100, where 0-10 gives a hostile reaction, 11-89 a neutral one and 90-100 a friendly reaction.
Hostile creatures will try to attack you, neutral creatures will let you be, and friendly creatures may help you if you are attacked. However, their personal relationship to other individuals and factions also matters. Typically, a person will rate as friendly to all other members of their faction.
That means that if you face two hostile bandits, and charm one into neutrality, that charmed bandit will still try to protect his friend if he is attacked. And as his friend is hostile to you, he'll seek to get into a fight with yourself.
In short, the environment around the charmed creature still colours his actions.
I don't know what was the matter in this case as you didn't describe the situation but it might well be somewhat like this.
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