Sometimes i get into a condition where my turn seems to end early. For example, production had stopped on several of my cities and it seemed like each time I added something to the build queue of one of these cities that my turn would end. So I wound up with an invading army crossing several territories and attacking my well defended research conclave without ever actually seeing the army on the way in.
Auto-turn is turned on. Go into options and deselect it. You'll have to manually end every turn, but you will not have that issue.
On a game-related note (but probably a second bug), when I muster an army out of a city, it's (a) tedious and ( confusing. I have to muster each company out individually, and every time I muster out a company I have to flip control back to the city to muster out the next unit.
Hold down ctrl button and continue selecting units. On a successful selection all the selected units will have a brighter ring around them. Once you have selected all you want move them all out at once. Note, it is also very helpful to remember your max army size when moving units out. If you forget, maybe just move two out to begin with, you'll see number of empty slots, and then just take that many more.
Is my turn ending when I muster out a unit? I do not think so, but I am not sure.
It shouldn't be, if you are only moving them to a square touching city. If you move them further than that, it may end your turn if you don't have any other active units with turns remaining, with auto-turn on. Again, your best bet is turning auto-turn off. Your turn will never end until you press the turn button (or hit 'enter' button, which also ends turn.)