From the typing spec:

The type tuple[Any, ...] is special in that it is consistent with all tuple types, and assignable to a tuple of any length. This is useful for gradual typing.

And mypy does precisely this:

type Ge0 = tuple[Any, ...]

def ge0_to_0(shape: Ge0) -> tuple[()]:
    return shape  # ✅ true negative
def ge0_to_1(shape: Ge0) -> tuple[int]:
    return shape  # ✅ true negative
def ge0_to_2(shape: Ge0) -> tuple[int, int]:
    return shape  # ✅ true negative

Ok, so far so good.

The typing spec also says the following:

If an unpacked *tuple[Any, ...] is embedded within another tuple, that portion of the tuple is consistent with any tuple of any length.

So tuple[int, *tuple[Any, ...]] is assignable to any tuple with int as first element. But mypy behaves differently:

type Ge1 = tuple[int, *tuple[Any, ...]]

def ge1_to_0(shape: Ge1) -> tuple[()]:
    return shape  # ✅ true positive
def ge1_to_1(shape: Ge1) -> tuple[int]:
    return shape  # ❌ false positive
def ge1_to_2(shape: Ge1) -> tuple[int, int]:
    return shape  # ❌ false positive

full output:

main.py:17: error: Incompatible return value type (got "tuple[int, *tuple[Any, ...]]", expected "tuple[()]")  [return-value]
main.py:19: error: Incompatible return value type (got "tuple[int, *tuple[Any, ...]]", expected "tuple[int]")  [return-value]
main.py:21: error: Incompatible return value type (got "tuple[int, *tuple[Any, ...]]", expected "tuple[int, int]")  [return-value]
Found 3 errors in 1 file (checked 1 source file)

So it's only the last two errors that are false positives.

mypy-play

Some observations:

• This is the case with (at least) mypy 1.15.0 and on the current master branch.
• It does not matter if you instead use tuple[Any, *tuple[Any, ...]] and/or use Any in the return types.
• Pyright behaves correctly here (playground)