When does "Across the sea" take place ? From the use of latin, probably not before the 8th century BC. But on the stone cork, there are cuneiform writings, which are older than that, and the writers have stated that the cork was created AFTER "Across the sea" ... So ? My guess ? We are witnessing, once more, the time-travel properties of the island.
The MIB, after being transformed, may have tried to use the frozen wheel again ... and sent the island back to, say, 5000 BC, which is the time of the older writings, and the next few centuries may have occurred twice on the island. Which would explain why no egyptian monument is visible in "Across the sea", even if the height of the egyptian civilization occured way before the roman one. The egyptian settlement could have happened after "ATS" in island time, but before "ATS" in global time. Huh, am I making sense ?
Or ( since I've theorized the "smoke monster" the egyptians associated with Anubis was Mom, not the MIB ) it may have been the wreckage of Claudia's ship that has been transported back to 5000 BC or before, like the freighter doc's body was time-displaced. OK, how could Mom speak latin, then ? Hey, she's got mystical powers, right ? So I'd say it's not a problem.
Or it's a plothole. But why would they have bothered to say "ATS" predates the cork, then ?