You know that that means that there was too few people left after a mission to handle all the promotions

? So those at the nearest base gets promoted instead. Figured it out after one of my bases almost was sacked by Etherals.
But think of the "Join XCOM!"-posters...
"Great pay! Few chances of making friends! Survival rate of standard-procedure missions lower than 50%!"
Oh boy. Guess your recruiters had to lie a lot

.
But, how did you manage Cydonia? How many were left?