I also run into this problem a few times. it won’t take me long though, to figure out which ones are safe to abandon for now. F.ex. a quest in another zone that you can take again near flightpath, when you come back later. Cool thing is, that alot of the times the future guide tells you to pick it up again anyway.
Edit: might be a good idea to not use auto accept quest but only auto turn in. Saw another post about the auto pick up guide only quest might be bugged.