Map bonus quests aren't completing

Solution 1:

Looking at the map modifiers (only 1% quantity) means you're running a normal version of the map as opposed to magic or rare. You won't complete the bonus objective unless it is done at a certain rarity depending on the tier of the map. To make it magic just use an orb of transmute on any normal map. Maps can be crafted with the same orbs as weapons and armor. If you get map mods that you don't like you can reroll them to get something more desirable.

If you open up the Atlas and hover a map it will show you this box seen below with the bonus objective. In the case of tier 1-5 (white maps) it is completing the map while it is at least a magic rarity. Tier 6-10 (yellow) require completing at least a rare version, and tiers 11-16 (red) require rare corrupted maps. Once done you get the checkmark and the yellow ring you see around your channel and flooded mine.