Does using cheats early for affection can cause bugs in the game like she will not join your harem or something else.Every character maxed has 2 to 3 sex scenes but when I did max them early the did not have them all or they come as the story goes.And last when the aff is maxed the npc has a cut scene but when I used cheats early for affection they did not have a cut scene is this a bug?
No, that isn't a bug, that's you breaking progression.
There is an order to how affection works and if you do it too early with a save editor or whatever it breaks that progression.
A lot of affection scenes are tied to story events so you going ahead of the story will break that.
That's why people say if you are going to cheat just do XP and gold or you may break your game.
Only way of fixing yours now is starting again.