They thought I had been robbing people.

[FalaGringo]

The use of the past perfect continuous in combination with "Thought" does not seem to be a popular choice without an indication of time, am I correct?

Present continuous / present perfect

1. "I am / I have been robbing people."
2. "I am / I have been talking to my sister."

Simple past + past continuous

1. "You thought I was robbing people."
   
2. "You thought I was talking to my sister."

Simple past +_past perfect continuous

1. "You thought I had been robbing people."
   
2. "You thought I had been talking to my sister."

 

[tedmc]

does not seem to be a popular choice without an indication of time

What do you mean by that? Your sentences are all possible. You could add "since" to indicate the starting time of the on-going actions.

 

[FalaGringo]

For example

"You thought I had been talking to my sister for the last 4 years."
"You thought I had been robbing people for the past 3 months."

So when we don't indicate a long duration of time, we tend to avoid "Had been" and use "Was" instead.

 

[Tdol]

We often avoid the past continuous because it's wordy. However, your sentences all work.