I have noticed that ships do not immediately gain the ability to upgrade after gaining enough experience.  It appears that the ship has to move or wait for the next month.

The first screen snapshot below shows that my Instigator has 26 experience immediately after gaining 5 experience for surveying an anomaly.  It also shows that the experience necessary for the next level is 26.  However, I cannot upgrade my Instigator.

The second screen snapshot shows that, after going to the next month, my ship is now able to upgrade.  It seems to me that, when a ship has gained enough experience to get an upgrade, players should be able to upgrade their ship, not wait for the next month.