I think some of the monsters would have definitely come from Dark Force, but not all of them. Some of the bad guys in the final dungeon were the magicians that served Dark Force in PS 2 and 4. You know, these guys?

So those guys are definitely DF related.
The biomonsters on Motavia in PS4 were grown by machines from Seed's complex. They didn't just appear because Dark Force was around (well, they did, because Zio tampered with Seed's machines, but you know what I mean).
One thing about machines in PS is that they are made to last. Lots of stuff in PS3 and PS4 is still running great after more than 1000 years. I don't think it is far fetched to say there are old labs or factories out there running on automatic and still churning out monsters and cyborgs. And like Rune said, some of the monsters could also be descended from Laya's originals that have gone out into the wild.
I think Cille's dome is the only place where the war is said to still be active before Siren and Lune return. There's two castles there (I can't recall the names... not Cille, but the others) where people talk about fighting each other with cyborgs and monsters.