You might be looking at the total number of squads available rather than the number of troops you have. As you complete research, the number of troops in each squads will increase (whenever you do a squadsize upgrade research). As a result, the number of squads you have will decrease, assuming you still have the same number of troops.
For example, you start off with 600 archers and a squad size of 6, or 100 squads of archers. With the first squadsize research your new squad size will be 9, so if you neither built more troops nor lost any in fighting, your new number of squads (the one you see when you look at the army camp) will now be 600/9 or 66.7. You did not lose any troops, you just have fewer squads because each squad has more troops.