Hello Everybody!

I'm watching the "Outcasts" TV series. In the first episode is (more or less) about a space transporter, which is trying to land on a new planet. When they finally have voice contact with each other, they are saying these lines:

Man from planet: What's you status, Captain?
Captain: We've got a couple of higher than normal protocols on the right side of the ship. Fatigue damage.
Man from planet: It's important you deal with that. Heat stress on atmospheric entry has been an issue for some transporters.

And then later, when the transporter is about to entry to the atmosphere they are saying the next few sentences:

Captain: We got, we got unusual stress readings, Carpathia, we gotta move protocols.
Crew man: Captain, that protocol's not working. We've got a stress burn in our right.

Basically I know what protocol means, but in these two cases I'm lost a bit.
Can anybody explain to me the meaning of "protocol" in these cases?

Thank you in advance for your help!