TYPICAL ERROR The horse was missing and his owner thought it must have been stolen.
CORRECTION The horse was missing and his owner thought he must have been stolen.
EXPLANATION It does not matter whether an animal is referred to by its actual gender (as a he or a she) or as an it. To be logical, the writer should choose one method of referring to an animal and keep to that method. The sample sentence above refers to 'his owner' and then refers to the horse as an it. The sentence could be corrected either by changing it to he or by changing his to its.
While the convention of using pronouns of female gender for ships, planes, other sorts of vehicles and countries is being used less and less nowadays, if pronouns of female gender are used, the same logic applies to them: they need to be used consistently.
Change these passages so that the gender of pronouns is consistent.