Yes there were
Persephone: "The come from a much older version of the matrix, but like many back then they caused more problems than they solved."
Here, much is the keyword telling us that they are not just one or two versions prior to the current, i.e., sixth version of the Matrix, they are from an even older version of it.
The question of where these exiles were hiding is not addressed yet we are given several points to make healthy conjectures.
Neo: Programs hacking programs. Why?
Oracle: They have their reasons, but usually a program chooses exile when it faces deletion.
Neo: Why would a program be deleted?
Oracle: Maybe it breaks down. Maybe a better program is created to replace, that happens all the time and when it happens, a program could either choose to hide here, or return to the source.
So, they can hide in the Matrix, i.e., they don't need to be smuggled with the Trainman, as they are already in. Also, they don't necessarily need the help of the Merovingian as well. For example, to the best of our knowledge, Smith never had any help from the Merovingian, although he was an exile.
While I have addressed how they survive deletion, the question of how they survive when that version of the Matrix is rebooted is still open. Yet, Oracle also offers some possible explanation, those programs might be hacking into other programs that would survive the reboot or strong programs other than the Merovingian might be harbouring them, like the Oracle harboured Sati or Seraph.
How Merovingian himself survived the reboot of his version of the Matrix is unknown. Therefore, whether Merovingian had any dealings with Seraph or other Seraphim when he was not an exile is unknown. Although this is pure speculation, knowing Merovingian it makes sense that rather than deleting capable programs, he might have started to accumulate them, even when he was the operating system. Here I have speculated that Persephone might have helped Merovingian to acquire these programs.