This has happened to me in both 0.87 and 0.90 (one time each).

After settling on a tile with my sovereign, casting spells on the city (each time this has happened it was on a tile with essence), picking a research path (Civics each time) I will then click the build tab to start building structures in my city. My sovereign's unit would be 'outside the city'-that is the unit slots where you see the iconic representation of the militia, hero, sovereign, etc when you click on the city would be empty. When I double click on a building to construct it, the sovereign's army would then go into the city. It is somewhat annoying because I will have to hold 'Shift' and click on each unit to get them back out of the city to explore.