First of all, there should be a tutorial when we start out for showing how the map works. So many people ask about where X system is or where X sector is when the quest info almost always clearly states the sector and system.
Secondly, people don't tend to read mission info very well, and cannot find certain information as well as things being hard to find (E.g. Starbase 24 rally point, the marker is off the map even when fully zoomed out).
To fix these things there are a few things that can be done both by player and by Cryptic to help people find their way around, and will be explained below:
It seems people need to know the difference between a "Sector" and a "System" and then how to find such things on the map.
If you know the sector a system is in, you only need to look for the sector on the map (Indicated by grey writing E.G. "Regulus Sector") and then head to the sector block that sector is in. After that you can look in the system's list or hunt around the map, either way works, for the system you have to head to.
It can be confusing at first, but in OB I managed to figure it out after a few missions and people should be given this information from the start. Some people will have trouble figuring out this info at first.
A simple tutorial with pictures of the map and with highlighted areas showing how to navigate around it would help new players quite a lot, as well as a simple statement or something saying to read through any quest/mission info and find locations they have to go to or something.
Another thing to add is more of a player side thing which the tutorial should mention or be made clear in mission info. People need to read quest/mission info more carefully as to find out the sector and system it takes place. Pretty much EVERY mission tells which sector and which system to head to. Maybe these could be highlighted in a different colour or something.
One more thing is that maybe quests/missions could be highlighted on the map more clearly, such as the "Make Primary" button highlighting the target system (Sector map) and sector block (Galaxy map) on the map in gold like the marker that is added in the quest info. The same as when on Starbase 1, the Admiral's Office and other objectives should be marked more clearly on the map.
Just to add to quest markers, I think something better than a white circle should be used for marking objectives in some cases, maybe shade the target area on the map red or something and add arrow on the map to guide to marked areas if area on the map i off the screen where the player is currently looking (On the map view). Such as in Starbase 24 mission, people often cannot find the Rally Point marker because it is a bit "north" on the map and out of view even when fully zoomed out.
Small things like these make it much easier for new players to navigate around, and many have quite som difficulty.