Hi,
I noticed that in your geometry optimization, you fixed the strain in the x- and y- directions, while not in the z-direction. I think this is a mistake. For such a 2D material you should rather fix the strain in the z-direction and relax it in the x- and y-directions like:

`constraints = [FixStrain(x=False, y=False, z=True)]`

Try to re-run the geometry optimization with this constraint and the recalculate the DynamicalMatrix.
Additionally, phonon calculations might require more accurate setting than 'normal' calculations. For this you might consider decreasing the tolerance as:

```
iteration_control_parameters = IterationControlParameters(
tolerance=1e-05,
)
```

Regards,
Troels