The way War Commander was coded ensures that units don't really disappear; the only way a unit leaves an account is if the player takes action to remove it. Sometimes units can be misplaced, though, whether through player error or a technical issue. Luckily, those "missing" units end up in only a few places:
1. Check all your squads in each your platoons. Each platoon can have up to 4 squads in it, and it can be easy to miss units in your 2nd, 3rd, and 4th squads. Be sure to check each squad, as that's the only way to see all the units in the platoon.
2. Single-use heroes can sometimes confuse players, since unlike normal hero units, they get used up; this can lead players to think the units have gone missing. They haven't; they've been used up! As the name implies, single-use heroes are good for only one battle instance. Single-use heroes have a red border to differentiate them from their regular hero unit counterparts, and they're grouped together in your Storage. Remember, these aren't normal hero units: they're good for one use. If you have a single-use hero in a platoon and deploy that platoon in battle, that single-use hero will be used up--you won't see it again after the battle, so plan accordingly.
3. Are you checking the right tab in your Storage? If you're on the wrong tab in Storage, the unit type you're looking may not show up. For example, if you're on the Storage building's "Standard" tab, the list of available units will not include units that are usable only in PVP battles.
Likewise, if you are on the wrong platoon type in Storage, you may not see the unit you're looking for, as only units legal for that platoon type will show up. If you're working on an air platoon, for example, you won't see any of your land units (see below).
4. Units placed in your Armory don't count against your capacity, but they also don't show up as options when you're building platoons in your Storage building. KIXEYE customer support can't even see units once they're in your Armory (not unless we log into your base and check it ourselves), so before ticketing in to report a ground unit lost, be sure to check your Armory; you might have forgotten you put the unit in there.
5. There is a known issue in which sometimes, heavily damaged PVP platoons will disband. Those units are not lost; they're simply in your Storage. Once those units are repaired, you'll be able to put them back into a PVP platoon.
6. A handy trick for finding a misplaced unit is to use your Workshop. First, open the Workshop...
...then click on the unit type you're missing (it doesn't matter which design you pick)...
...then click "Equip," as if applying a design to the unit...
...and the Workshop will tell you where the units of that type currently are! This works for every building except your Armory; the Workshop can't see in there, so be sure to check in manually.