I don't know if this can be reliably reproduced in all systems, but I rolled an Eridani with multiple mining stations, and things went kind of wrong. I talked to one station and got a mission to chase off miners at an illegal claim. Then I went and talked to the other two and got two more similar missions. However, only the mission of whichever station I talked to most recently was displayed on the HUD and map, and *none* of them showed up in the mission log, only the starting "reach the core" and "finish what you're doing and then talk to Benedict" missions.
I don't think the mission log is consistently used for all missions. I believe only main story missions are logged.
The HUD only highlights one target at a time, but all targets exist and are stored. No glitch there, there's just only one variable for 'player's current target'.
The mission log is used for missions made after it was implemented. So this isn't a glitch, but something that needs to be upgraded....a lot of older missions have unusual patterns in them (eg. habitat "clear X station" missions in Eridani only get offered once unless you take mining missions in between each of them and don't dock at habitat for any other reason). Upgrading to the newer system would definitely be good though, as it'd allow for mission stacking and more complex systems in the future.