One player was using Millinium to essentially negate any plot card played. however there was the argument that unless the plot card is intended to stay in play, like magical weapon or romance, Millinium cannot target it.

Basically we need to know if playing a plot card that doesn't stay in play, unlike a plot card, is considered putting it 'in play'

I've always ruled that Millenium can cancel any ONE advantage card when it's placed on the table.

This means that cards that are not intended to remain in play for longer than one battle (AKA cards put into play during the battle phase) can and in many cases should be the targets of her ability. She is one of the strongest Arcane Characters with this reading of the rules however in a 3-5 player game her power diminishes greatly.

Moreover, her power cannot affect advantage cards that are already in play such as a Faction played last round.