I just ran into the bug on my second play through. The first time I played the game I never had this problem. The second time, the Little Sister just stood in front of the 2nd test subject after finishing. For whatever reason the script didn't get triggered to force her to move to the next test subject. I had to reload from the autosave at the start of the level. That time there were no problems, and the trainer was enabled (inf health/eve active).
The first time I seeded the entire area with proximity mines after the first Little Sister was killed at the 1st test subject. I did this before going and getting a second Little Sister. This might have screwed something up by killing splicers as soon as they spawned. Second time through I just killed them with the rocket launcher and shotgun when they got within range.
Disabling the trainer didn't work for me when I encountered the problem. The problem I had was after the splicers attacked while the Little Sister was harvesting the 2nd subject. After the last one was killed the script to trigger her to move on never fired. Tried a save and reload without the trainer and it didn't help. I had to restart the level. After restarting the level I reactivated the trainer and everything went fine. On my very first play-through of the game I never encountered the problem at all, so it seems to me to be either entirely random or some very specific combination of circumstances.