This error solved!
Actually, this was not error but I got confused by how input_values method of Wav2Vec2Processor works.
speech_array, sampling_rate = sf.read(row.file)
# speech_array.shape = (8900,)

input_values = processor(speech_array, sampling_rate=16_000).input_values
# input_values.shape = (1, 8900)

However, when you use it with huggingface datasets, it will return 1D array
def prepare_dataset(batch):
    batch["input_values"] = processor(batch["speech"], sampling_rate=16_000).input_values
    
    with processor.as_target_processor():
        batch["labels"] = processor(batch["target_text"]).input_ids
    return batch

dataset = dataset.map(prepare_dataset, remove_columns=common_voice_train.column_names)
# np.array(dataset[0]["input_values"]).shape = (8900,)