Okay, well there's 2 different parts to this question.

1. I don't know if it is confirmed when season 6 will be set.

2. People believe Simmons is pregnant because we know of Deke. Therefore making children a possibility. We're not sure when but it might as well be during the series. Also, she did randomly vomit halfway through season 5, so....reasons to believe?

However, there really hasn't been much reason to believe that she is, it's not discussed much.

@Bennyhef234 Chloe or Clark (I can’t remember) said in an interview that season 6 takes place a year later, it doesn’t really make sense for the actors to lie about that, it is also why they changed a lot of the characters hairstyles (to show the time that has passed). It has also been confirmed Coulson will be dead by the time season 6 starts.

As for the other thing Elizabeth said that Simmons was just kind of grossed out by the fact that she brought her grandson from the future. Also that even she was confused and initially believed Simmons was pregnant and that the writers cleared it up for her.

And it’s not so much talked about here then it is on reddit and Twitter.

if Jemma were to become frozen somewhere within the timeframe between the 2 seasons, any pregnancy of hers could theoretically become suspended. and if she was thawed sometime after the freezing, the pregnancy might theoretically resume from the suspending point.

those might be one way for Jemma to become pregnant by Leo and still be pregnant a year later.

or if she spends a considerable amount of time in outer space, she would be aging at a slower rate than on Earth; and theoretically any pregnancy would progress at a slower rate than on Earth.

@Mdsb759 Yeah you are right I guess, I’m the 100 (a cw show) they chose to do something similar. I don’t think they will make Simmons pregnant yet because honestly what is the point. Maybe in like the end of season 6.? Also why would she go into CRYO sleep, she doesn’t have the chamber Fitz has it.