tl; dr: you have unaccounted-for resistances in the circuit, especially the 9V battery itself. These add to the network and thus reduce the real current you're seeing compared to your ideal model.
Let's start with the battery since this is the primary culprit. 9V types have a fairly high internal resistance, several ohms at least. For their intended application to power low-drain loads (tens of mA), this isn't a problem. With a 10-ish ohm load like yours the voltage will droop quite a bit. Things will get even worse as the battery ages.
Related: Why can't I power everything with a 9 V DC battery?
Knowing your 9V battery's weakness, you can do a couple of things:
- Account for the droop: Measure the battery voltage under load and use that in your simulation.
- Reduce the current: Consider scaling up your resistor network values by 10x or 100x to make them more reasonable for the 9V battery.
- Reduce / eliminate the droop: Replace the battery with a regulated power supply.
For (1), it's best to measure the voltage right at the points where the current enters and exits the resistor network. This eliminates the voltage drop in the wiring.
For (2), your battery droop will be reduced a lot, but you will still have some, see (1).
For (3), an inexpensive power solution is a USB power supply (5V). These hold a steady 5V that's reasonably well regulated. If you have more money to spend, a lab supply with meters would be even better. Might be worth it if this exercise and others like it will be a regular part of your curriculum.
Besides the battery, there's a few more error points in your real vs. virtual components:
Resistors have a tolerance. This is specified when you buy the resistor. Common tolerances are 5% and 10%.
Wires have resistance. Figure about 0.25 ohm for a typical 24" meter lead. Two of them will add half an ohm or so.
Multimeters have shunt resistance. They measure current by inserting a shunt resistor and measuring the voltage drop across it. For a Fluke 77 the shunt is either 0.5 ohm on the 400mA input or 0.037 ohm on the 10A input.
How to calibrate things? To see where you stand on accuracy, start by using your meter to measure the overall network resistance, minus the power leads. Then, apply your power and measure your current + voltage. Use this to calculate your 'real' resistance. The difference will be your unaccounted-for resistances in your battery, leads and meter shunt. Add this resistance to your sim and see what you get.
Somewhat unrelated, that’s a simulator I haven’t seen before. I tried it and, honestly, I found it to be a bit clunky. It wasn't wrong; it did give the right result for the 'ideal' case. But it seems lacking in information. And its library seems very limited.
Have you looked at the Falstad circuit simulator? Like yours, it's web-based, provides interactive visuals, and is easy to use. One really handy thing Falstad does that your sim doesn't: mouse-over any element and it tells you its current, voltage, power and other info.
Speaking of which, here's your circuit in Falstad (simulate it here):
Mouse-over the power source, it gives current. It also shows the resistance it's seeing in its load.