I work as a stationary engineer now, it's rather boring as the trade has become fully automated. Basically I sit there in the utility-room office watching an automated supervisory screen and reacting to situations... by reading other screens. I dispatch the other tradesmen (mostly electricians and e-techs) to make repairs and adjustments that the computer can't deal with.
We burn fuel oil.
Most of the time we refer to the storage and delivery system as "the fuel" rather than "the fuel oil system." Thus when we had a pump shit itself at 4am during a cold snap at peak steam delivery hour (facility laundry and overnight sterilization) I had to tell MY boss: "Something's wrong with the the fuel at the moment, the mechanic's working on it, should be back up within the hour."
So there is real world precedent for technical people using shorthand, I know other facilities like ours have their own shorthand and language. It is entirely possible that " ... Somehow the antimatter in the warp drive pods has been deactivated."
is referring to to the entire system being rendered inert. Cold shutdown, venting, and restart lockout of the entire antimatter system. Rather than elaborate on that in a time-crunch they simply say "antimatter has been deactivated." If and when they need more information they'll ask for it (how? why? repair?) or check the diagnostics themselves.