Translation:I thought you had talked to him.
While "talked to him" is perfectly correct English, "spoken to him" seems more fluid to say. Entretanto, ambos são corretos.
The verb in the principal clause determines the use of the past subjunctive in the subordinate clause. This is formal Portuguese, so there are always exceptions to the rule.
Using the past subjunctive probably indicates that what you expected to happen (talking to him) didn't occur.
As Duolingo has gone for the indicative here, are we to assume the speaker is certain that the 'talking to him' had taken place ?
Yes. Whitlam's Modern Brazilian Portuguese:
"Eu pensei que" can be followed by the indicative tense when there is a degree of certainty in what you are thinking.
• Quando ele disse isso, eu pensei que ele era um cara sério.
"Eu pensei que" is followed by the imperfect subjunctive when what you were thinking turns out to be mistaken.
• Eu pensei que ele fosse um cara sério, mas acabei me decepcionando."
Yet again, emeyr, I thank you for your help with the subjunctive! Perhaps eventually I will get the hang of it's use or non-use: one can but hope.