If, during a thunderstorm, you use the command "/toggledownfall", then the weather will seem to clear at first and it will stop raining, but lightning will continue to strike even after you've used the command (and the sky will remain darkened), as if it was still raining and a thunderstorm was still occurring. Exiting and reopening the world causes the lightning to stop. Possibly caused by the fix to MCPE-17295.
My theory is that lightning is not directly/properly tied to the current weather, which would explain why thunderstorms will stop when you exit and reload a world and why this bug happens.
I can confirm this is an issue in 0.16.1 also.