Well, indeed she was pregnant during that time. It's not uncommon in the entertainment industry for actors to be pregnant while filming. In Kaley Cuoco's case, during 'Based on a True Story', the production team had to make certain accommodations. For example, they might have used different camera angles or looser clothing for her character to hide the pregnancy if needed. And she was still able to deliver a great performance regardless of this situation.
As of my knowledge, there's no indication that Kaley Cuoco is pregnant on 'Based on a True Story'. Usually, such details would be reported in entertainment news if it were a significant part of the show, but I haven't come across any such news.