In my game, no active secondary quest will show a marker on my map, and oftentimes the object of the quest will never spawn, eg. the treasure drops from Dark Brotherhood prisoners. I noticed this after an hour of playing after I got the first bugged objective, and by the time I realized ALL secondary objectives were bugged, all my saves had already overwritten the ones from before the problem began. Can someone help? Has anyone been having the same problem?

You know you have to set both the category and the actual quest to active at the same time to get the markers for these to show up right?

Also, make manual saves (often!) from the ingame menu. These won't be overwritten.

In you're journal under Miscellaneous both that and the objective need to be selected in order for quest trackers to appear. If that's not it then yours is a bug I've never heard of before. I'd recommend investigating console commands for a solution.