Is this spike in the direct output of the encoder? I would suggest that you try several encoders and see if they all have the problem. If they do, try some other brand or model of encoder.
Some bandaids would be to use a LC low pass filter to get rid of the spike. Another would be to make a circuit that looks for a zero lever of over a certain time duration and puts out its own pulse on the next rising edge. This could be a simple sequential state circuit with a clock. It could go to the next state for each low value and after a certain number of them goes to a state that looks for the high level and puts out a pulse and then goes to the rest state.