When creating a new fleet in a system which provides free levels— for example, when creating a new Iron Hands fleet using the Telesterax in Medusa, or when recruiting Imperial Navy fleets using the Schola Progenium in Cadia— the admrial ship gains the correct bonus levels, but any subsequent ships do not.

I found, however, that upon completing a battle, after switching your admiral to the underleveled ships, or upon the end of the turn, the ships gain the bonus levels back. This leads me to assume that the ships had the levels applied correctly, but the bonus levels aren’t showing up on the gui unless I force an update on the ship gui (by completing a battle, switching around the admiral, or ending the turn).