✔ 最佳答案
其實呢個問題唔係咁複雜。
先澄清左樓上一點：「steal 是一個短暫性動詞,不是可以持續一段時間的動詞, 不可以接在has/have/had 后」
試下用 google 搵 "has stolen"，可以搵到超過 1.4 million 個例子。我再作一個：
How can you make any excuse for him? He has stolen my money!
present perfect 講已經發生o既事，影響至今，有乜唔得？上例o既影響就係「我冇左ｄ錢！」（now the money is gone!）
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睇返問題本身，兩句都係 passive，你唔清楚之處係
１． passive voice
２．而係 tenses。
先講 passive voice 結構，其實只係原句主要動詞（即講係乜野動作o個個，如 walk，dance）之前，多左個 be 或佢o既不同變化，即係：be, is, am, are, was, were, been, being
例子：
John kicked him. => He was kicked by John.
只要主要動詞前加上 be，將主要動詞本來o既形態（呢句係 past tense）套用於 be 度（咁 be 就變成 was），再將主要動詞變成 past participle，同埋 subject object 換位，咁就成句變成 passive。多個例子，留意動詞 tense 變化：
The dog is barking at Simon. => Simon is being barked at (by the dog).（is 不變，只係加左 be，佢繼承左 barking o既 ing，而 barking 則變成過去分詞 barked）
所以，had been stolen 同埋 had stolen，其實都係 past perfect tense，只係前者係 passive，後者 active。
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依家可以講 tenses。就以你o既答案講：
I think Tom's watch had been stolen by his neighbour.
past perfect tense 用於有兩件事一先一後發生，咁較早o既一件用 past perfect 講，而較近o既一件用 simple past。如：
I had already cleaned the room before he came.
但呢句中你可以話冇一件較近o既往事，所以用 past perfect 就不恰當。平日我地想講一件往事，只要用 simple past 即可。所以答案先會係：
I think Tom's watch was stolen by his neighbour.
即係話，如果呢句係想講隻錶係o係某事發生之前已經失竊，咁就應該用 past perfect，如：
I think Tom's watch had been stolen by his neighbour before he left home.
