It's a little tick-box thingie below where you type in the Save Name, which I'm thinking defaults to an off (un-ticked) state. So I don't think it's very easy to do an accidental Save of that, but you may have.
Since you say you are doing the Stock game, I'll guess (probably incorrectly) then that you're later in the war, like into 1944 maybe, and have had a few recent trips to Empire Waters (off of the coast of Japan). The Stock game has nasty habit of spawning ships on top of ships (the RGG) in the Jap_HarborTraffic file, besides the fact that it is constantly generating patrol vessels in the harbors. If you go into the Inland Sea in mid-44, you'll find about twice as many vessels as there were there in 1943. It should be the opposite.
This is the nature of the game in Stock trim if you play a long career. Throw in a few planes, and there can be quite a bit of data to keep track of, just in the Jap_HarborTraffic file. Hence the bigger Saves after a few "years" of playing the game. Also, if you used to have mods activated, they do not always de-activate cleanly, and that can add more "trash" to your Save file. Use the "Tasks..." in JSGME whenever you first install the game, and "Generate a snapshot of the game files". Then install your mod. After you de-activate the mod, do a "Compare game files to snapshot", and make certain that all is well. It takes several minutes each time you do that, but worth it in the long run for the aggravation it might save you later...
