There is a problem with rally points. When I try to use them, I keep getting notified that there are idle ships. This seems to be caused by 2 problems.
First is, ships don't tend to make fleets when they move to the same destination. If there are no ships at the destination, they don't seem to realize they can or should join fleets. They need a ship to be there in order to join a fleet, otherwise they go to the same square and idle. Its like "move to destination", and "move to destination and join fleet" are 2 very different commands.
The other problem is that ships don't join fleets after the first fleet is full. So if you had 30 ships going to the same destination, but your fleet size only allows for 6 in a fleet, you're going to get 1 fleet of 6 ships and 24 ships outside of fleets.
There is no money warning in place when upgrading a lot ships at once. When you use the commands tab to upgrade ships, it will upgrade all of them immediately. There is no warning that it'll cost this much to upgrade all of them, and no warning if it'll leave your account balance in the negative.
When upgrading ships individually, they don't tell you how many turns it will take. If ships are far away from your planets or starbases, it can take many turns to finish upgrading.