He also says something along the line of 'I hope you and your children rot in hell' after John brings him to the jail. John and Abigail's daughter was born after the gang disbands because he mentions it to Bonnie, 'I have a son, and I had a daughter, she died, and years before that I was in a gang' so I have no clue, I guess Javier must've kept checks on them, although Im not sure why

It's clear that he kept tabs on the Marstons. My question is, how? He was in Mexico by 1907 and it's extremely unlikely that he'd come back to America.

I imagine when Bill fled to Mexico, he and Javier probably talked to each other about what has been going on. Bill would have been much more able to keep tabs on John

I think it’s a continuity error. Considering the daughter aspect as well, I think Rockstar forgot about this for RDR 2. Once he returned to Mexico, I don’t think Javier returned to America, and even if he did, there’s no reason why he’d spy on John.

As @TimmysMaName95 said, Bill may have told Javier about it. Perhaps he heard gossip about a man at Beecher’s Hope who was forced to work for the government or something. Still, a desperate explanation when it seems to be a continuity error.

While I can't neccesarily prove it, I think it's possible that Javier reunited with John in between time-skips in a similar manner that John met back up with Charles and Sadie. Maybe John invited Javier to live with him at the farm and mentioned his kids during small talk, but Javier still wasn't able to accept it. John mentioned that when the gang fell apart, Javier had took it the worst. There's no doubt in my mind that John met up with him at some point and got to see how his brother declined from the noble revolutionary to the stone cold hitman.