User blog comment:B214/Chapter 504: Rift/@comment-7418318-20161001212543

There was something I couldn't quite reconcile and thus thought of as stupid and that is that Natsu didn't notice that Lucy was alive. With his super-sensitive senses he should literally be the last person in the series to make such a mistake.

But it does make perfect sense actually, IF he checked her before knocking out Dimaria. Because if Dimaria stopped time, naturally Lucy's heartbeat and breathing would also be frozen. And if Natsu doesn't know that Dimaria can stop time (which he shouldn't) it's not surprising he mistook this absense of life-signs as death.

And once time resumed he was too enraged to pay attention to his sharpened senses.