When I start and stop the bot a lot this happens to me more often. At the start of a season I do this a lot with 4 bots all running together... I will stop one while the others keep going to do gear upgrades.
The oddity is that one bot that I just stop/started will be having navigation server issues.
I have found that closing the bot and opening a new instance of it seems to solve the issue when this happens.
If you're having it constantly, there may be another issue with your connection or firewall. Perhaps contacting support would be your best option in that case.
Unless you see a big outcry in the forums, usually the nav server itself isn't actually down.