Debugging I2C, Effect of Oscilloscope Probes
new

I would be curious to know if a 1MHz snubber at the Rx would reduce NAK error rate.

C=560pF in series with 220 Ohms across Rx to 0V. Some adjust may be necessary.  e.g. 500 Ohm 270 pF



old info

I2S uses 74HCTxx or TTL logic thresholds.  I2C uses std CMOS thresholds.

If the Vcc of each endpoint is floating, connecting a scope probe with an inductive long ground lead adds a common mode voltage (0V) than may differ from the "floating" ground and due to CM noise coupling at each end , some differential voltage can result. 

It is hard to assess your CM noise without measurements between each ground with a current shunt.

The cable will have 100pF/m or so of capacitance and adding 10nH/cm of scope ground clip can induce a resonant impedance that may cause ringing.  

So investigate noise ingress and experiment with earth grounding at either or both ends of the communication.  Also, consider twin probes in A-B for signal integrity such that when both probes are on the same signal it produces a flat line. ( Vdif=0)

Depending on cable lengths and bit rate, a CM ferrite transformer can help raise the CM impedance to radiated noise.

The R pull-up depends on cable capacitance and bit period vs risetime and amount of noise ingress.

http://www.ti.com/lit/an/slva689/slva689.pdf