It sounds like you inadvertently learned the MyQ hub's universal transmitter to both door openers for one of the hub's opener controllers.
You will need to erase all learned transmitters for the second garage door (usually a press and hold of the opener's learn button, see opener's manual) and then relearn all your remote transmitters (in cars) and relearn MyQ Hub's transmitter (press and hold door image in MyQ app to bring up configuration screen).
To resolve this issue, your MyQ hub needs to be programmed to operate both Overhead Door openers independently. This needs to be changed on the garage door opener itself, though, not the hub.
You'll need to clear the memory on the secondary door and reprogram the remotes and hub back into it.
Let me know if you have any other questions.