I've noticed a bug where if my lead Pokemon faints in battle, it will still appear to be following me after the battle - but if I turn and talk to them, it acts like the Pokemon that's actually supposed to be following me. It will refresh to look like the correct Pokemon if I go through a map...
The new cycling through the party update works great.
I still have an issue that pops up every now and then - not game breaking. But when walking over certain events - for instance, the OverheadLights event or anything that the player can normally walk on top of, the following Pokemon will not...