Lisa's segments made pretty clear that she didn't tell Joe at first because she didn't think he could actually handle the entire situation that is Coil.
Later, when she realized he probably could handle all but one aspect of it all, she was a little worried by how his mentality/thought process kept changing as his powers grew, meaning she couldn't figure out what his plan/reaction might be...
and she was completely terrified of that one aspect Apeiron might not be able to handle, named Noelle, absorbing Joe and spitting out evil copies of him.
If Joe's power wasn't so out of context, she'd be right, and because it's so out of context, she has no way of correcting her position, or even knowing she should until after the fact.