The makers of the original Planet of the Apes film sequels clearly did retcon the logic for why Taylor and his crew ended up in the 40th century.
The first film suggests they spent 2000 or so years travelling through space, while ageing only 18 months due to relativistic time dilation, an effect predicted by Dr. Otto Hasslein.
LANDON: That means we've been away from Earth for 18 months.
TAYLOR: Our time. You've gone gray. Apart from that you look pretty chipper
for a man who's 2,031 years old. I read the clocks. They bear out Hasslein's hypothesis. We have been away from Earth for 2,000 years, give or take a decade.
Planet of the Apes (1968)
It was also implied that they were on a mission to establish a new population on a distant planet, so they presumably weren't expected to return to Earth, or at least not within the lifetime of anyone they left behind.
TAYLOR: Did I tell you about Stewart? Now there was a lovely girl. The most precious cargo we'd brought along. She was... to be the new Eve. With our hot and eager help, of course.
Planet of the Apes (1968)
Conversely, the first two sequels suggest Taylor and his crew were expected to return to Earth within a year or two their departure, and that when they failed to do so, a rescue ship was launched to find out what happened to them (a rescue ship which then jumped forward 2000 years or so through a "defect" in time that Taylor's ship also passed through).
BRENT: Of course I know who I am! I'm an astronaut! I was sent here on a rescue mission. To find a fellow astronaut, Taylor. We're from this planet, but from another time, 2,000 years ago. I know, I... I know I sound insane. And it's my insanity. No, no, I don't know how to get back. We came through a defect, a slippage in time. That's what must have happened to Taylor. I'm sure he tried to get back.
Beneath the Planet of the Apes (1970)
THE PRESIDENT: Yesterday, a U.S. spacecraft splashed down off the Southern California coast. It was one of two that have been missing in space for over two years now. To be exact, the one commanded by Colonel Taylor.
Escape from the Planet of the Apes (1971)
The primary reason for this change was likely Charlton Heston's reluctance to return for the sequel. He didn't think there should be a sequel at all, and only agreed to play a small role in it out of a sense of obligation to the producer, Richard Zanuck.
CHARLTON HESTON: Dick Zanuck called me. He said "Chuck, we have to do a sequel, you know. This film is enormous." I said "I don't want to do a sequel. That's like the Andy Hardy series." And he said "Chuck, I can't make the sequel if you're not in it." And I said "Well, you got me, Richard, because we couldn't have made this film if you hadn't given it a go. So how about if I'm in the sequel but I get killed in the opening scene, and you pay me whatever you want and we'll give it to a school or something?" He said "OK, that's fine, that's a deal." And then, as the script developed, he called and said "Chuck, how about if we have you disappear in the first scene and then you're killed in the last scene?" And I said "Yeah, I guess. OK, fine. What the heck."
Behind the Planet of the Apes (1998)
During early development of the first sequel, several story proposals were submitted featuring Taylor as the protagonist. But since Heston was only willing to play a small role in the film, a new story was required, built around a new protagonist.
Had they gone with someone native to the 40th century -- such as Cornelius or Zira -- they could've stuck with the first film's logic for why Taylor ended up in that time period. But since they chose to go with another 20th century astronaut, Brent, as the new protagonist -- likely because they wanted a character in the same mould as Taylor -- it then became difficult to avoid contradicting the first film to some degree. After all, why send a rescue party looking for Taylor and his crew within two years of them leaving Earth, if they weren't expected to return for centuries, if at all?
The filmmakers were probably counting on most audience members not remembering everything that was said in the original film, since the first sequel was released two years later, and there wouldn't have been a VHS release of either film back then.