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Like any software, chess engines can have bugs or issues that may affect their performance. These bugs can range from minor issues that do not significantly impact the engine's play to more significant problems that may cause the engine to make mistakes or produce incorrect analysis.
One example of a bug that has affected chess engines in the past is the "50-move rule bug," which occurred when the engine incorrectly counted the number of moves made in a game and declared a draw due to the 50-move rule being reached, even though the rule had not actually been satisfied. Another example is the "threefold repetition bug," which caused the engine to incorrectly recognize a position as a threefold repetition, leading to a draw being declared when it was not warranted.
It's important to keep in mind that chess engines are not perfect and can make mistakes, just like human players. While it's generally a good idea to rely on chess engines for analysis and guidance, it's also important to use your own judgement and to be aware of the limitations of the engine.
In recent years, newer chess engines have been developed that are faster and more powerful than older engines like Stockfish. These newer engines often use advanced techniques such as machine learning and neural networks to improve their analytical abilities and enhance their performance. While Stockfish is still a strong engine, it has indeed been surpassed by some of these newer engines in terms of speed and analytical ability.
I believe Lichess' software had a three-fold repetition bug at one stage. I distinctly remember a draw being declared after my opponent moved his king back and forth between two squares in order to force an (erroneous) draw a few years back.