The Man team tries to be careful about revealing their identities and personal information around Frankini, but not so much around Goomer; however, Kid Danger identifies a picture of Kris Hart as his mom.
It's clear that Captain Man needs Frankini, but there's no reason for bringing Goomer along, who, as a henchman, could potentially cause a lot of muscled interference.
No details are given as to what circumstances Captain Man and Kid Danger were able to take Frankini and Goomer out of prison.