Mass effect 3 Missions Bug (SPOILERS)

Having an issue in ME3 where missions don't disappear from the journal if completed, OR impossible to complete.

I completed the Eden Prime: resistance sidequest during the from the ashes dlc, and the hacker sidequest from the omega dlc, and the mission did not mark as complete in the journal

Similarly, i FAILED to complete the mechanic side quest on omega, and it did not remove itself from the journal even though it could no longer be completed.

HOWEVER, the largest issue is that the Tuchanka: bomb mission. I allowed it to time out (accidentally. i don't hate krogan lol). ORIGINALLY this meant that many krogan died, and the mission was no longer completable. However, in the LE, I received the email from Wrex saying the bomb detonated and killed a lot of people, however, the mission is still in my journal, and still listed on the map, and further I CAN STILL UNDERTAKE THE MISSION despite the fact the mission should have expired.