I saw you come in yesterday.
I saw that you came in yestarday.
is there any difference between these sentences in meaning?
If you saw (past tense) something happen (base form of verb), you were there and you observed the event directly. I saw you crash your car yesterday - I was there at the time and observed the event.
If you saw (past tense) that something happened (past tense), you saw, after the event, a sign, or evidence, that it had happened. I saw that you crashed your car yesterday - I saw it wrecked by the side of the road as I passed by.