I've seen two different situations crop up:
1) Units don't seem to save their group size properly, so a Company reduced to 5hp (1 man) when loaded from the save game is turned into a single troop.
2) Units moved into a city (and possibly other situations that grant bonus HP for defense) get their size recalculated permanently.
It seems like there's some shortcuts being taken in tracking group size. Somewhere the game is calculating number of troops in a unit by dividing unit HP by troop HP and rounding off. That would be fine except for one big problem: in some critical places it's using current unit HP/troop HP where it should be using max unit HP/troop HP. This is especially noticable with cities, where it's exacerbated by the fact that bonus fortification HP are added to max hp but not current hp.
This is more a symptom of the bigger issue with how groups are handled: rather than being sets of discreet units (like, say, MoM), they seem to be just a big monster with stats equal to a base trooper times X, and the calculations for stats vs. X go both directions, causing all sorts of mess.
