Need help to analysis & overcome an issue with LM358 OP-AMP
If you are measuring a 0.1 ohm resistance then, reversing your formula, you expect to measure an output voltage of 29.9 mV. The first "notable" thing is that you are getting quite close to the lower permissable limit for the LM358 (20 mV above ground).

However, you should also note the input offset voltage for the LM358 - the data sheet states it as having a maximum value up to 7 mV. There will also be resistor tolerance effects these will add more error.

Try altering the model file for the LM358 to see if there is an input offset voltage value you could tweak to better understand the problem. Also try increasing the supply voltage - the LM358 is "said" to operate down to 3 volts but there is little information in the data sheet that tells you how it might perform.