Some phrasal verbs are separable and some are inseparable. I'm sorry to say that there is no rule for distinguishing between the two types. They must be learned one by one. "Come across" is inseparable; therefore, "I came across him yesterday" is correct. (Since you included a specific time in the past in your sentence (yesterday), it would not be correct to use the present perfect tense.) I know this wasn't the answer you were hoping for. Sorry.
