Well assuming that's true - I'll check it out in my next game start - if that's the only case where this is true then we're again in the not an issue case. You have a single ship and it's not doing anything productive. Otherwise, if you have even 1 other ship, then the AI is splitting the stack in 2. And then if both are doing the city thing then your entire fleet isn't doing anything productive, same kind of "not an issue".
As soon as one ship is doing something productive then some AI ships will hunt it down. And no, you can't "go back to port" or it will be intercepted. Something productive is away from your port and close to the enemy. There you can't swap ocean, and lose the trail. As soon as you go back you're hunted, exactly like now.
So... Either not an issue (former) or not a change (latter)?
As soon as one ship is doing something productive then some AI ships will hunt it down. And no, you can't "go back to port" or it will be intercepted. Something productive is away from your port and close to the enemy. There you can't swap ocean, and lose the trail. As soon as you go back you're hunted, exactly like now.
So... Either not an issue (former) or not a change (latter)?