I just assumed that all of the others before Kyle and Jesse were killed, due to being failed experiments. After all, that's what Kyle was... and they tried to kill him.
I also think that they made them in pairs (Kyle and Jesse, Specimen X and Specimen Y), as opposed to individually, probably to see if there was anything different on the gender front or something. Or... maybe even to make a failsafe if anything like one of the specimens had escaped. After all, Jesse and Kyle are connected mentally somehow.
I was wondering about the girl, but I figure it was just one of those dumb things that they forgot to explain to us...
I was also wondering about Jesse's hair. It was very long, because she'd been in the artificial womb her entire life... but, then, why wasn't Kyle's??
Just another thing to think about.