Audio problem: When Luke says, "Now all we gotta do is find this Yoda, if he even exists," if you look closely, his mouth never moves.
Audio problem: In the Special edition, after Luke frees himself from the cave in the beginning, he stumbles towards the exit. You can hear his lightsaber go off, but it stays firmly on. Cut to him emerging, and now his lightsaber's off. (00:09:30)
Audio problem: When Luke is about to leave Dagobah, he says, "But Han and Leia will die if I don't," but the words don't match the movement of his lips. (01:19:45)
Audio problem: At the beginning, when they close the door of the hangar, it makes no sound on the first shot. (00:11:45)
Audio problem: When Chewie is choking Lando, Leia says "We understand, don't we, Chewie?" A shot later, her mouth moves but no sound is heard, and when she says "We don't need any of your help", her voice is heard a little bit after she starts moving her mouth. (01:42:20)
Audio problem: When Luke and Vader are fighting in the carbon freezing room, at one point Luke forces Vader off the side, looks around, then jump down himself to look for Vader. Listen to the sound that is supposed to be the sound of Luke's feet hitting the ground; you can see Luke stand back up after jumping over the side in the bottom left corner of the screen, but Luke is almost full stood back up when we hear the sound of his feet hitting the ground. (01:45:20)
Audio problem: After Han goes to the command centre during the battle on Hoth, Leia says to a controller, "Send all troops in sector twelve to the south slope to protect the fighters," but the words don't match her lips. (00:30:35)
Audio problem: In the carbon freezing chamber, Han says to Chewbacca, "The Princess - you have to take care of her". When he says, "You have to take care of her", his head is shown from behind, but the motion of his jaw doesn't match the words. (01:35:35)
Audio problem: When Han punches Lando, his hand never makes any contact with Lando's face, and the sound effect is heard after his hand goes past it. (01:29:20)
Audio problem: When Lando is punching desperately at the door's control panel in Cloud City, he says "The security code has been changed!" but his mouth doesn't move when he says it. (01:47:10)
Answer: The short, short answer to this is "Yes... from a certain point of view." The long answer is complicated and depends completely on what timeframe you mean by "always." If you're going back all the way to the early rough drafts of the early-mid 70s (which actually resemble Episode I more than they do the Star Wars of 1977), you'll find there's a cyborg father figure protagonist that makes a heroic sacrifice, and then another character that is a "black knight" villain that eventually turns to the side of good near the end. Just to make things more complicated, there is yet another character, a villain by the name of "Darth Vader" that is a human Imperial officer like Grand Moff Tarkin. It may be a stretch to count all that as "Darth Vader was always the father" but the pieces were all there, at least.
TonyPH
(1) Now the earliest explicit mention on any documented material that Darth Vader is Luke's father comes from notes Lucas made outlining the general story of the trilogy and its place in the larger Star Wars saga. These were found in the archives for The Empire Strikes Back, but they are undated and we don't know if they were written before Star Wars (1977) and carried forward, or if they were written afterward. These were found fairly recently (made public in 2010) and as far as I know Lucas has never commented publicly about them.
TonyPH
(3) One thing we know, at least, is that Lucas had come up with the idea of Darth Vader the father before starting work on The Empire Strikes Back. Something incredibly odd, though, is that the first draft written by Leigh Brackett does not feature the twist (and in fact introduces Anakin himself as a ghost); for a long time many fans took this as proof that Lucas hadn't thought of the idea at all by then, but after the series outline was discovered it was made apparent that Lucas simply hadn't told Brackett for some reason. Perhaps he wasn't sure yet that he wanted to go through with it, or maybe at that point he was thinking of revealing it in the third film. Either way, Lucas would write the second draft himself, and that's where the twist first appears in script form.
TonyPH
(2) Something that must be understood about Star Wars (1977) is that it was an ALTERNATIVE to his original plans of a saga. By then he didn't think it was realistic that he would be able to make a long series of many movies, so he came up with a "Plan B": he crammed the general story of the trilogy into one movie. So we know that when Star Wars (1977) was filming, Darth Vader was NOT Luke's father, because this one movie was IT, that was the whole story. But what we DON'T know, is whether that means Lucas had abandoned the idea of Vader being the father in order to simplify the story, or if Lucas simply hadn't thought of that at all just yet.
TonyPH
(2, cont.) On a side note, you can tell by watching Star Wars (1977) how it has condensed the story of the trilogy. The middle portion has the characters trying to escape capture from the Empire while one of them loses a duel with Darth Vader (like The Empire Strikes Back) and the third act is a final battle against the Death Star above a forest moon (like Return of the Jedi). The first act features a member of royalty on the run while a couple of protagonists find the main hero on a desert planet, resembling the original drafts and by extension Star Wars: Episode I. Because of this we've arguably never actually had a "pure" first chapter to the original trilogy, even though Lucas eventually had the film serve this purpose anyway.
TonyPH