Why do we see unused port in U2300A/U2500A with similar waveform and frequency but with lower amplitude to its adjacent or close by used port?

It is recommended to ground all the AI connection that is not being used. If you have multiples of AI channels to be used, one good way is to have alternate connection. Example is AI101, AI103, AI105 are connected to ground whereas AI102, AI104 are used to acquire data. This way, your signal line is 'surrounded' by ground.