cable or accessory is not certified and may not work reliably with this iPhone

You haven't mentioned whether the device was connected to anything when you received the message or for that matter what it was connected to.

First thing to try is to reset your device. Press and hold the Home and Sleep buttons simultaneously until the Apple logo appears. Let go of the buttons and let the device restart. See if that fixes your problem.

Try checking your cable socket/lightning cable for dirt, grime, pocket lint, etc. I could not find the solution to this issue myself and after much searching I found someone stating that cleaning this out helped them immensely.

After taking a wooden toothpick (making sure the phone was OFF first) and gently clearing out the edges and inside of the lightning socket this went away.) It is worth noting that I had a significant amount of dust or lint buildup along the edge rails which I think was causing the iphone to believe it was plugged into something when it was not.

Try it and see, ensure you are very careful and do not use any conductive tools to clean the area in question. Compressed air also does wonders here.