Voltage spikes on Arduino Input affecting digital and analog readings
I will take a SWAG with the data provided. From what I think you are saying you have pins from the Arduino connected to the outside world, this is a NO-NO. What you seeing is exactly what I would expect to happen. There is a lot of information available online on how to do this interface. My systems were 24VDC and in an industrial environment. I  would use a 20K for R1 to be sure I had at least 1 mA through the contact to keep it clean (old school). This circuit will filter out a lot of garbage and survive large voltage transients. It is slow, about 120ms. You could try 12V and change R1 to 10K. For the analog signals I suggest you digitize them before sending to the arduino. More information such as line length, sensors, etc along with links to technical information to them would help a lot in giving you a better answer.