Nope, I make sure not to be using Neo while I have the trainer running. Seems like it's fairly safe, but I didn't want to take unneeded risks.
Ran into the same issue at the end of Chapter 5 as well, where it would quit the auto battler after every battle. Thankfully it was right near the end, so I didn't have to actually do much myself.
Either way, not an issue for me anymore since I finally finished off InSaNe. Pretty sure I got the worst prize, but oh well I have a shiny new trophy at least.