Two past tenses together in a sentence - I *had assumed* you were dead

You replied quite late. I had assumed you were dead.

I have heard that two past tenses shouldn't be used in a sentence. What's the rule regarding that? Please clarify.

Answer

See this.

Note the pluperfect form. To quote from the definition of pluperfect makes what's going on here clear:

The pluperfect is a type of verb form, traditionally treated as one of the tenses of certain languages, used in referring to something that occurred earlier than the time being considered, when the time being considered is already in the past.

In your example, the speaker is referring to a time in the past when they assumed that the person in question was dead. Maybe their assumptions changed, maybe they're just discussing a past event. An example to clarify:

Jim and Sally were discussing the terrifying event. Sally said "It was dark, I was scarred, so scarred. I lost you, and you never came looking for me." Jim replied "I'm so sorry, I had assumed you were dead."

As opposed to:

Jim and Sally were running through the thick night away from the angry mob. Suddenly they stumbled, and Sally fell away into the dark. Jim waited to hear some sign of where she had gone, but there was nothing. He got to his feet and continued running, fighting back tears because he assumed she was dead.