If a card states something (i.e. perform a 2 full astern, or perform a sensor echo) and the ship it is attached can't perform said maneuver/ability, is this a case that the card text grants the ability.
From my understanding all of the below examples would fall under the "Breaking the Rules" section on page 18 of the rule book and that the cards text would override the general rules.
Examples (by no means is this an exhaustive list):
Jadzia Dax Allows a 2 forward or Bank - Ship doesn't have a bank
Double back allows a full astern 1 or 2 - Ship doesn't have a full astern maneuver listed
Picard Manuever allows a ship to perform a 5 forward after performing a 3/4/5 forward - Ship cant perform a 5 forward
Evasive Pattern omega allows a sensor echo - ship is not cloaked (Which rules state a ship must be cloaked to sensor echo)
Gul Dukat stats the ship can perform a free battle stations from his ability - Ship doesn't have a battle station option