First, the circuit cannot work as shown because you bias it to 0V while providing only +12 and 0V supplies. Consider if you apply +10mV to the input, it should be amplified by -470/3.6, about -100, so 10mV positive input should result in -1V (negative) output, which is not possible without a negative supply to the opamp. As such, your circuit will not work as a linear amplifier for any positive or AC coupled signal (negative input voltage would work, but opamps tend to perform poorly with inputs shorted to rail).
Second, when you add 100nF plus your source impedance which may be reactive due to long leads or similar, you will get a different phase response than with a pure short (in your simulation). There is also a difference between simulating with signal injected at the opamp input, which looks at stability of the amplifier itself, amd breaking the loop at the feedback resistor, which looks at stability of the feedback loop.
The reason why your simulation works may be due to unrealistic behaviour of the opamp model. These often contain voltage controlled voltage source, and other ideal spice elements, making them representative only when your surrounding circuit respects the operating limits of the chip.