Mutations break after aws-amplify/cli update: "input contains a field that is not defined"

### How did you install the Amplify CLI?

npm install -g @aws-amplify/cli@12.10.1

### If applicable, what version of Node.js are you using?

21.7.1

### Amplify CLI Version

12.10.1

GraphQL transformer version: 2

### What operating system are you using?

Windows

### Did you make any manual changes to the cloud resources managed by Amplify? Please describe the changes made.

No manual changes made

### Describe the bug

After upgrading from `@aws-amplify/cli@12.0.0` to `@aws-amplify/cli@12.10.1` I am unable to do any mutations. All of them return the error: `"The variables input contains a field that is not defined for input object type 'DirListInput' "`

### Expected behavior

Carry out the mutation successfully without throwing an error as it did in `@aws-amplify/cli@12.0.0`

### Reproduction steps

I am running a react app with `"aws-amplify": "5.3.17"`

1. (simplified) schema.graphql:
```graphql
type DbDirTable @model(timestamps: { createdAt: "createdAt", updatedAt: "modifiedAt" }) {
id: ID!
createdAt: AWSDateTime!
modifiedAt: AWSDateTime!
dirList: [DirList!]!
copiedFromId: String
}

type DirList {
id: ID!
items: [DirListItem!]!
title: String
colour: String
}

type DirListItem {
id: ID!
note: String
visited: Boolean
}
```

2. After running `amplify push --y` it changed:
```
src/API.ts
src/graphql/mutations.ts
src/graphql/queries.ts
src/graphql/schema.json
src/graphql/subscriptions.ts
```

The difference in those files was that it added `__typename` to every type, input, mutation and query

3. Then I call
```ts
await API.graphql>(graphqlOperation(updateDbDirTable, { input: inputData }));
```

where inputData is:
```ts
{
{
"id": "3894a81b-4e93-4627-aae1-0a0617a8ed75",
"dirList": [
{
"id": "a9cb6ec9-0254-4d37-ac96-e25e46f50a42",
"items": [],
"title": "One",
"colour": null,
},
{
"id": "09701984-fe07-4140-b36a-c9ecd8ca0549",
"items": [
{
"id": "6535fb67-f55d-475c-b32d-065f5b26f4ee",
"note": null,
"visited": null,
}
],
"title": "Two",
"colour": null,
}
]
}
```

But it throws the error
```json
[
{
"path": null,
"locations": null,
"message": "The variables input contains a field that is not defined for input object type 'DirListInput' "
}
]
```

4. `updateDbDirTable` is auto-generated in `src/graphql/mutations`. I am not using any custom resolvers or overrides

### Project Identifier

_No response_

### Log output

```
# Put your logs below this line

```

### Additional information

If I discard changes in the graphql the code in step 3 works ok

If I downgrade to 12.0.0 and re-generate the graphql files the code in step 3 works ok

Same issue on 12.4.0 because it adds the same changes as 12.10.1 to the auto-generated graphql and API

**I noticed that if I keep all of the regenerated changes and only discard the `src/graphql/queries.ts` then the code works ok**

The **only** new change in `src/graphql/queries.ts` is that it added `__typename` everywhere.

This is strange since all my queries, when called directly, work fine with the newly generated file and they fetch the data ok.


### Before submitting, please confirm:

- [X] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.
- [X] I have removed any sensitive information from my code snippets and submission.