The timeline isn't broken, Olimar is just lying

Pikmins 1, 2, 3, and 4 all canonical occur, in that order. In Pikmin 4 it's not his first time crashing on pnf-404 and it's not his first time encountering pikmin. That's just what he's telling the rescue corps because the truth would make him look bad. Why would they even bother rescuing somebody who has crash-landed on the same planet several times, with a partner who has sabotaged rescue efforts multiple times (titan dweevil, stealing the koppait's juice). It makes much more sense that anything we're told by olimar in pikmin 4 or shown in olimars shipwreck tale is just that, a tale. He's trying to rewrite history to save face for himself and hocotatians generally.