Bouncing at some points in square wave
Noise can come from anywhere, most likely due to mutual inductive or mutual capacitance coupling between traces on the PCB or cable and another signal. 

The first thing that needs to be done is to determine which frequencies are important to the design. In otherwords, what kind of rise times do you need from the hall effect sensor. 

The second thing would be to determine the frequencies from the noise, if the two signals have different frequencies then a filter could be used to block the noise from getting into the hall effect sensor signal.

Another approach would be to prevent the noise from coupling to the signal at all, proper shielding and routing techniques can be used to prevent coupling. Use shielded cables if the sensor is off board and proper routing on the PCB (don't run the traces from the hall effect sensor next to other noisy traces.)

There is an off chance that the noise is coming from the hall effect sensor itself because it is detecting a magnetic field that is changing, if that is the case, then filtering will need to be used to filter out the unwanted noise.