Repository: transformers
Issue: Paliegemma Pad Token not Masked
Labels: bug,Multimodal,VLM

### System Info

- `transformers` version: 4.48.0
- Platform: Linux-6.1.92-3-x86_64-with-glibc2.31
- Python version: 3.10.15
- Huggingface_hub version: 0.26.2
- Safetensors version: 0.4.5
- Accelerate version: 1.1.1
- Accelerate config:    not found
- PyTorch version (GPU?): 2.5.1+cu124 (True)
- Tensorflow version (GPU?): not installed (NA)
- Flax version (CPU?/GPU?/TPU?): not installed (NA)
- Jax version: not installed
- JaxLib version: not installed
- Using distributed or parallel set-up in script?: parallel set-up
- Using GPU in script?: Yes
- GPU type: NVIDIA A100 80GB PCIe

### Who can help?
@amyeroberts @molbap
**Description:**

I encountered an unexpected behavior while using the Paligemma model. Specifically, the pad tokens' attention masks are being processed to zero (i.e., unmasked status) during the execution of the `self._update_causal_mask(attention_mask, token_type_ids, past_key_values, cache_position, input_ids, inputs_embeds, is_training)` function.

After investigating, I found that this behavior stems from a change in the code between the latest version (4.48.0) and the previous version (e.g., 4.43.0). The order in which the pad tokens are masked has been reversed, leading to inconsistent behavior, especially when using left padding.

### Code Comparison

**Latest Version (4.48.0):**
```python
if attention_mask is not None:
    causal_mask = causal_mask.clone()  # copy to contiguous memory for in-place edit
    mask_length = attention_mask.shape[-1]
    padding_mask = causal_mask[:, :, :, :mask_length] + attention_mask[:, None, None, :].to(causal_mask.device)
    padding_mask = padding_mask == 0
    causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
        padding_mask, min_dtype
    )
    # we are training thus we need to create a full mask on the image + prefix but causal on suffix
    if is_training:
        causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
            token_type_ids[:, None, None, :].to(causal_mask.device) == 0, 0
        )
```

**Previous Version (4.43.0):**

```python
if token_type_ids is not None and labels is not None:
    # we are training thus we need to create a full mask on the image + prefix but causal on suffix
    target_length = cache_position[-1] + 1
    causal_mask = torch.full(
        (sequence_length, target_length), fill_value=min_dtype, dtype=dtype, device=device
    )
    if sequence_length != 1:
        causal_mask = torch.triu(causal_mask, diagonal=1)
    causal_mask *= torch.arange(target_length, device=device) > cache_position.reshape(-1, 1)
    causal_mask = causal_mask[None, None, :, :].expand(inputs_embeds.shape[0], 1, -1, -1)
    if attention_mask is not None:
        causal_mask = causal_mask.clone()  # copy to contiguous memory for in-place edit
        mask_length = attention_mask.shape[-1]
        padding_mask = causal_mask[:, :, :, :mask_length] + attention_mask[:, None, None, :].to(
            causal_mask.device
        )
        # unmask the prefill
        causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
            token_type_ids[:, None, None, :].to(causal_mask.device) == 0, 0
        )
        padding_mask = padding_mask == 0
        causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
            padding_mask, min_dtype
        )
```
**Issue Details**
In the latest version (4.48.0), the pad tokens are first masked using the padding_mask:

```python
padding_mask = padding_mask == 0
causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
    padding_mask, min_dtype
)
```
However, when the following block of code is executed during training:

```python
if is_training:
    causal_mask[:, :, :, :mask_length] = causal_mask[:, :, :, :mask_length].masked_fill(
        token_type_ids[:, None, None, :].to(causal_mask.device) == 0, 0
    )
```
the pad tokens (which have token_type_ids == 0) are unmasked again, effectively reverting the previous masking operation.

**Impact**
This behavior is particularly problematic when using left padding, as the pad tokens end up being unmasked in the latest version, whereas they were correctly masked in the previous version (4.43.0).

**Question**
Is this an intentional change, or is it a bug? If it’s a bug, could you please provide guidance on how to address it? I’d be happy to help with a fix if needed.

Thanks for your support!

### Information

- [x] The official example scripts
- [ ] My own modified scripts

### Tasks

- [ ] An officially supported task in the `examples` folder (such as GLUE/SQuAD, ...)
- [x] My own task or dataset (give details below)

### Reproduction

```python
from PIL import Image
from transformers import AutoProcessor, PaliGemmaForConditionalGeneration

processor = AutoProcessor.from_pretrained("path")
model = PaliGemmaForConditionalGeneration.from_pretrained("path")

prompt = ["<image>caption en","<image>caption en wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwww"]
labels = ["123123123123","456456456456"]
image_file = ["image path"] * 2
raw_image = [Image.open(i).convert("RGB") for i in image_file]

inputs = processor(text=prompt, images=raw_image, suffix=labels,
                    return_tensors="pt", padding="longest")
model(**inputs)
```

### Expected behavior

The pad tokens end up being unmasked.