i have seen it often too, at first, i did not believe in it either, because it is hard to explain. but i saw and heard about it a lot.
jealousy is probably the reason. it could be over anything, skin color, look, height, clothes, families.. education... you name it..
in her case, it sounds like running late or something minor were just excuses. She (the boss) is collecting evidence to build her case, so she can fire her eventually, or overpower her.
i would leave, this environment is very unhealthy.
