Transistor internal resistance
Unfortunately we know nothing of your actual simulation. But here's something that can be usable:

There's a semiconductor junction between the base and the collector. Actually there's also one between the base and the emitter and the base is so thin that the junctions must be taken into the account as one in a special way working strucure (=transistor).

Semiconductor junctions nor transistors do not obey Ohm's law, the relation between current and voltage is much more complex than I=U/R where R is a constant. The commonly used exponential relation is known as Shockley's diode law.

Semiconductor junctions can often be considered as a series circuit of a diode and a resistor. The resistor explains comfortably why the exponential current law of diodes do not be valid at high currents. I guess this resistor is the one you have just found. But that's a guess only. 

In analyses which try to predict how microvolt or millivolt range AC signals would behave in diodes or transistors when they are riding on substantially larger DC voltages one can calculate and also measure dynamic small signal AC resistance which depends strongly on the idle state DC current and voltage (=the operating point).

ADD after the question was edited to have questioner's simulation circuit but before another edit where the claimed 99 Ohm CB resistance was changed to be CE resistance:

The inserted image doesn't give a slightest hint (if all nonsense interpretations are excluded) how big resistance there is between C and B in the transistor. It doesn't either show internal resistance between C and E. The image shows that the transistor gets far bigger base current through R1 than it's needed to pull down the bottom end of R2. There's still 0,04V because transistors cannot work if there isn't at least a little voltage between C and E. You have driven the transistor to saturation - it's how this case would be generally described as words.

To understand something about how transistors work make R2 smaller. Finally the voltage between C and E starts to rise substantially because the base current isn't enough any more. To keep Vce still low (sub 0,5V) you must finally make R1 smaller to get more base current. Practical transistors can easily be destroyed by having too low R2 resistance, but in simulator that doesn't cost money.