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I wanted to tell my friend he had not picked up my phone because he was passing through some tunnel.

May I say...

"I had called you but you didn't picked my phone. I thought you would be passing through tunnel" OR
"I had called you but you didn't picked my phone. I thought you were passing through tunnel"

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The two sentences are a bit different and I will try to explain as I understand it.

Would (auxiliary verb, past of WILL) is used to unreal, possible or hypothetical situations, this verb is more polite, more imaginative, also it cannot be the main verb alone:

I would love to visit London. (a hypothetic situation)
Would you take my hand, please? (a polite request)
I'd suggest you to write it. (a polite request/an advice) [I'd = I would]

Were -ing (past continuous of BE) is used to situations which were happening at a special time in the past and none hypothetical, it is more direct, not imaginative. It's used to say "it happened while...", "it was happening". These sentences below are directs, they aren't polites (because more direct):

You were loving to visit London. (an emotion while you visited London, not anymore)
Were you taking my hand? (an action while something, yes or no question)
I was suggesting you to write it. (a request at a defined time)

In your sentence, you begin with the verb "thought" (past of THINK) which means you did not sure about what happened but you were elaborating a theory while he did not get your call:

He was passing through...   // situation while he did not get your call 

Otherwise, you said: maybe you did not have your cellphone in your hand, you had not enough battery, you lost your phone... - imaginative, polite:

He would be passing through...  // perhaps; this situation possible among others  

Therefore, you should use were -ing because while he didn't answer you thought that and it's a friend, then maybe you can avoid the polite form. Also, I think the correct sentence might be:

I called you but you didn't take my call. I thought you were passing through a tunnel.

I hope that I didn't forget something and this helps you to better understand the little difference between these two forms.

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What about "I thought you would have been passing through a tunnel"? I think it works in your hypothetical scenarios. – Kinzle B Apr 10 '14 at 5:59
@ZhanlongZheng You can, however, I see it more polite and even more hypothetical. Also, I wouldn't use this tense because, personally, I use it with an if-clause and there is always an unspoken "but..": "If you had not taken my call (but it was), I think you would have been passing.." – Fllo Apr 10 '14 at 15:30
(but it was) here implies that you did take my call, right? – Kinzle B Apr 10 '14 at 15:54
@ZhanlongZheng That's right. – Fllo Apr 10 '14 at 15:55

The correct use is decided by when you had that thought: if the thought occurred to you when (or before) you were making the call, then would be is an appropriate choice (were is still possible). If, on the other hand, the thought occurred to you after that event then were is correct, but would be is not right - a possible variant would be must have been. There are some other problems with your grammar, rather than deal with those individually, perhaps you can see them from the differences with this:

When I called and you didn't pick up, I thought you were passing through a tunnel.

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