Based on the screenshot you shared above, the issue is the PWM generator with the carrier-compare logic in the model. In this case the PWM carrier signal is limited by the model step size of the of the RT Box. The result is low PWM resolution and the current waveforms you're observing.
This scenario is described in a tutorial on the Plexim website: "RT Box: From Offline to Real-Time". I copied (and slightly modified) the relevant text below:
The reason is that the “Modulator” subsystem has the carrier-compare logic inside the model and is resolved within the window of the model step size (e.g. 5 µs), which is too little time considering the switching frequency.
To resolve the PWM gating signal with adequate accuracy, the solution is to use the PWM Out block to physically generate the PWM signal on the digital out port of the RT Box, connect the digital out and digital in ports together using a D-Sub 37 pin cable, then capture the physical PWM signals back into the box using the PWM Capture block. With this approach, the gating signal is generated and sampled with a resolution of 7.5 ns, and sub-cycle averaged over the model step size.
Please let me know if this helps.