I think you are confusing two different things.
There is a daily milestone that you can do once per day per character. This requires you to do the challenges at a certain location/activity: do 3 challenges in the Strikes playlist, do 3 challenges on Titan, etc.
There are also weekly milestones that you can do once per week per character. As of this writing, there are the following weekly milestones:
- Flashpoint: complete Public Events at a given location
- Clan XP: Earn 5000 clan XP (must be in a clan)
- Call to Arms: Compete in the Crucible
- Nightfall: Complete the weekly Nightfall Strike
- Leviathan: Complete the raid or raid lair
- Trials of the Nine: Compete in Trials matches
- Heroic Strikes: Complete 3 Heroic Strikes (requires Curse of Osiris DLC)
Based on your question, you completed two of the weekly milestones. These will reset and you'll be able to complete them again after the next weekly reset (Tuesday 1700 UTC / 1PM EDT / 10AM PDT).