I don't think this is unique to the Clarity. I stopped believing my 2012 Prius Plugin when it nearly dumped us on the side of a back road late on a Sunday night in a snowstorm. We reduced speed to 25 mph to conserve gas in hopes to make it to town, fortunately there was a just about to close gas station that saved our bacon. After that I never believed any estimates when it mattered. Look at the gauges not the estimates.
If EV range hits 0.0 it won't update that until range reaches 2.0. So that's why it doesn't seem to be charging when regenerating.