On the city screen, you need to look at the Special tab instead of the Buildings tab to find Military Academy. All buildings that cannot be built through hammers (<iCost> -1, including Shrines, Scotland Yard, Military Academy, and Menagerie) show up there. -1-cost buildings that are also Wonders (Shrines, Academy) also show up on the Wonders tab, but the Buildings tab specifically excludes any building with a -1 cost.

I believe its somehow related to new 50% fixed sliders and result is that my cities wont produce any science now. City screen shows that 50% commerce but science out put is zero (or actually 1/turn). Other visible problem is civic advisor, last three rule civic wont show at all because of too small box.