There are two multi-polygons a and A where a is supposed to be contained inside A. Using shapely, the following difference operator

b = a.difference(A)
print(b)

gives

POLYGON EMPTY

However testing A.contains(a) returns False; a.touches(A) also gives False.

How could this be possible with Shapely?

The wkt descriptions for A and a are hosted in the following Gist link (due to characters limit) https://gist.github.com/vodp/169b12f507a9730c0dd2ac86ca2589db