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what does the manual mean when it says it costs a unit so many points to enter an enemy hex?I understand the rest. The cost to enter and leave an enemy zone of control(ZOC) makes sense. The costs to move from one ZOC to another is given in terms of costs to enter an enemy hex. Does it mean the costs to enter the hex vacated by a retreated or destroyed unit in addition to the costs of attack?

It means just as you suggested - the movement cost to enter a hex previously held by an enemy unit or an enemy ZOC. You can see this very easy by toggling on 'e'.