Today I went and collected my pets from missions. I then selected a new mission. It was a level 50 Sanctuary of Saerielle mission. I then selected a pet to go on the 45 one and it said I selected a mission that didnt exist. Then I was able to select the level 50 mission again even though it said in the mission log I have a pet doing it. The level 45 mission then worked after. So I have two pets out on two different level 50 missions.

This is not a bug, in fact I do this every day to load up on six level legendary missions. There are five different missions at each level, one for each stat.

Missions refresh at the start of every hour, though there is a small chance that it will load the same mission. Thus, if you select a mission at say, 6:59 and don't press the submit button until 7:00, that mission might have cycled out.

My ideal mission rounds (in levels), to show:
Hour 1: 50, 25 (1h), 25 (1h), 25 (12h), 0, 0
Hour 2: Collect 4 1-hour missions, 50, 50, 25 (1h), 25 (1h), 25 (12h), 25 (12h)
Hour 3: Collect 2 1-hour missions, 50, 50, 50, 25 (12h), 25 (12h), 25 (12h), done for the day.

Usually it takes about four, though, because it sometimes lands on a mission I already have running.
In theory, if you had six or seven hours, you could get all 5 level 50 missions, but I don't usually have that time.

Ah alright. Not sure the exact time it happened, but that probably is it.