The counter for missions will not count as being complete. This has happen on any mission that gives an amount/percent to kill. I use my titan and it didn't count it until I log off for the night and came back the next day. Keeps dropping same level loot even tho my light level is higher than the drop (my light level is 351 but it keep dropping 340 loot). The game is also not increasing my light level even if i put higher level gear on. Instead it will decrease.