I've confirmed that this is a bug. If the levels for a line contour plot are all outside of the z limits, the levels are replaced by the lower z limit, here:

Here is a simple reproducer:

import matplotlib.pyplot as plt

z = [[0, 0], [0, 1]]
cs = ax[0].contour(z, levels=levels)
ax[0].set_title(f'levels_in={levels}, levels_out={cs.levels}')

levels = [2]
cs = ax[1].contour(z, levels=levels)
ax[1].set_title(f'levels_in={levels}, levels_out={cs.levels}')

fig.tight_layout()
plt.show()

Under most circumstances we'd get away with this behaviour. However, if there is a quad which has the lower-z value on 3 of its 4 corners then half the area of the quad is at the lower level and the contour line is calculated on the upper edge of this triangle (see #19691 for detailed explanation).

I presume that if the user specifies the contour levels then we should not modify them, even if this means that no contour lines are plotted. But I suspect there may be issues about colorbars being displayed without any contents?

Thanks @ianthomas23 for taking a look at this and providing an explanation. With this knowledge we can make a simple workaround in the user code by setting a new, artificial, localised minimum before plotting. E.g.

data[0, 0] = -1