From a physics engine standpoint, what is probably happening is that the bouncing object penetrates the other object and is pushed back out. When it is pushed back out, a velocity or force is applied to give a more realistic physics simulation (even without bounce). (Normal force of the contacting surfaces).
One thing that you might try to do is to set the velocity of the bouncing object to zero in the direction of the collision normal so it isn't coming back at you.
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