Yingluck, 46, arrived at the polling station near her house here and accidentally put it in the wrong box.
The ballot papers for party-list votes are orange, while the ones for constituency voting are purple. She placed the orange party-list ballot in a box with a sign in Thai which said 'constituency system'.
She did the same with the purple constituency voting paper, putting it in another box that said 'party-list system'.
It was only after Yingluck left the polling station that the press began to notice the irregularities in the photos they had taken.
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Many Internet users thought that Yingluck was probably too busy with posing and smiling for the cameras and did not notice that she was putting her ballots in the wrong boxes.
Others found the incident an embarrassing mistake and said it should not have been made by a politician with a position as high as prime minister.
Protest leader Suthep Thaugsuban, who has threatened to sue Yingluck for wasting taxpayers' money by holding the snap polls, was quick to take a swipe at her.
Yingluck has been facing months of opposition protests demanding her to quit, install and unelected People's Council and scrap the snap polls.