What's up with CARGO?

[Mercury]

Ok this is probably going to be a silly question, but I really don't understand the whole cargo thing.

I sail out, kill a couple ships, sail into port and get a pop-up window that gives me the stats of my voyage, including the value of my cargo that I plundered. Then I sail out again and usually it says my cargo holds are still full. One time, however, it said that my cargo was 0/3, meaning my cargo hold was empty (yes I am using the noob ship hehe).

Is this a glitch or am I just missing something when it comes to the whole cargo system. This noob ain't understading lol!