We had said him not to leave any message and call us anytime he wants , after two weeks he didn’t call and rather left one message for us .
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We had asked him not to leave a message, but to call us anytime he wanted. After two weeks he hadn’t called, but rather had left one message for us.
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I don’t dare argue with a moderator but I would write this sentence in the following way : We asked him not to leave a message, but to call us anytime he wanted. After two weeks he didn’t call, but rather had left one message.
I don’t want to seem ignorant (though maybe I am), but is it so important to use Past Perfect in the first sentence? And I don’t understand which action in the second sentence had been earlier (call or message). If you don’t mind I’d like to hear an explanation, plz. 
P.S. As far as I know in a sentence we have a “mistake” not an “error”.
Thanx in advance.
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I have just followed the original poster’s template, Maryann; presumably, he has a good reason in his context for using past perfect.
I see no serious semantic problem with using ‘error’ here. Here is the first definition at Dictionary.com:
1. a deviation from accuracy or correctness; a mistake, as in action or speech.
Trying to separate mistakes from errors is not an efficient use of language study time.
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Thank you for a quick reply, Mister Micawber. But I’d like to know if the variant I wrote was possible. As for the “mistake” and “error” I just mean that “mistake” is most frequently used in ordinary speech than “error”, isn’t it? And to my mind it would sound better if in this case we say “mistake”.
P.S. I’m opened to critics and grateful for it, it helps to improve myself in further studying
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I see nothing wrong at all with using the simple past, and it is certainly simpler and more usual-- but then your final past perfect sticks out like a sore thumb.
I can’t speak to the relative frequency of mistake and error; I have been using both of them too long on these fora.
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Yeah, I don’t like that final past perfect either, thank you so much for explanation.
Maryann
Thanks alot for your kind reply ! 