Megan Boone wears bulky clothing most of the time, and her love scene with Tom (Ryan Eggold) was carefully edited so that her face and belly were never in the same shot. This was due to her being about 6 months pregnant as of the air date. She gave birth to her first child in April 2016.
The scene involving the "FBI executive" being kidnapped is actually plausible. In a scenario such as was shown, someone with law enforcement training would remain with the armed agents. The FBI recruits mainly lawyers, computer techs, and accountants- not people with actual law enforcement experience.