I read #1 and #2 back to back. Gotta give Jubilee a break.
In issue #1, her first line to Apocalypse was "First of all, you're crazy if you think I'm bringing my son to see you." Why would she say that out of the gate... unless Apocalypse specifically asked to see Shogo? We don't really know what Apocalypse said to her when he called her. All we know is that he called her before Gambit even mentioned her.
She assumed he was safe in #2 until she had that dream. Maybe too soon to know for sure, but given Psylocke's own dream, it stands to reason there is a bit more to it. Her instinct was to get him away from Apocalypse.
Of course, then Betsy up and drags him through to Otherworld and now we got Shogo the Dragon. spoilers:end of spoilers
Take THAT, Kate.
I'm willing to wait and see how it all unfolds.