Sounds like a fun campaign Richard. It's normal especially if it is version 1.0-1.1 as Spartiate said.

I think bankruptcy means they can't train new units. But they can still keep them. The AI especially in earlier versions have the habit of the spamming the seas with ships - along with passenger armies. Only sea areas where you have ships or troops nearby are visible. So those ships can linger almost anywhere.

The AI ship-spamming was curtailed by patch 1.2