In recent games (since the Bonny Update, mid-October), both Javelin Throwers and Noble Javelineers have refused to upgrade to Crossbowmen or special units that replace the Crossbowmen. In one game, the Javelin Throwers finally let me upgrade once I had Musketeers.

In both cases, I had access to Longbowmen (either directly or via diplomacy unit sharing).

This is a big issue if you chooses either the Olmecs or Maya, as it renders all of your ranged units essentially useless by the early Medieval period.