Are you using your aperture wide open? If so, that might be your problem... you may want to close it down a stop or more if you are able to. The wide open apertures can be harder to nail the focus in low light.
Don't be afraid of getting super close to a window... and move your subject around until you can see the catchlights. I can't tell you the times we'll just be sitting somewhere and I'll look in one of the kids' eyes and say, "don't move, you have the most amazing catchlights right now!" LOL
I've learned where I can find the pockets of good light in my house... and now can spot "good light" more easily in other places.
And some folks just work better using a tripod at all times, especially in low light.
Not sure how helpful I was!