everything needs a waypoint because thats how the game decides the direction to point it (well normallly anyway because you can change that) but without a waypoint the game isnt allowed to fill in any gapsin data so you get the error dode.
not all errors are going to interfere with the mission working ok but you should eliminate all errors as a rule. sometimes like in ports you might have errors of ships too close together and such but as long as they dont spawn close enough to collide you are usually ok.
one problem i remember many complaining about is trouble getting ships to engage each other, sometimes they do and sometimes they dont.
you cant get carriers to launch aircraft, they just wont do it so forget any ideas in that area.
you should read this:
http://forums.ubi.com/eve/forums?a=t...846#5681008846