Because, yes, there are comedic beats throughout the end. Most of them surrounding a perfectly timed cut to Freeman and the scientists giving a "wtf" look. Because what is happening is so insane. So in that sense, there are jokes pertaining to how nuts the movie gets.

If you thought the end was a joke in the sense that it was irreparably stupid, odds are you were pretty disconnected from the moment she could start controlling her own matter, which was at, like, 20%. Freeman told us precisely where the movie was headed in his opening speech. The movie sets the rules for its own world and then follows them to a T.

I had no problem accepting that at 100% capacity Lucy could control her perception of time and space, because, well, it had been established. It's a superhero movie. If I'm not going to nitpick the science of Superman or the X-Men, I'm certainly not going to nitpick here-- especially when the world created is so consistently following its own rules.