Pretty sure its a bug. Check the issue tracker. Its not just crystals, all that type of raw material farming is like this, some stuff worse than others. Brain trees afaik are impossible atm. I gave up after 10 minutes of trying to pew off several different nodule things. Couldnt get a single one from any angle.
As a tip to anyone else that may find themselves here having similar problems. There's definitely a pattern of unhittable ones, and I think there is about 4 identical patterns that are unhittable. This at least helps avoid spending time on trying to hit them.
As a side note, I find that ensuring that lining up the "literal target coordinates" and yourself - such that you are aiming at the bulk of the object when firing, helps ensure you hit the most "exposed" part of the objects wireframe.
Basically, object/target is like this:. =o==>
And the targeting recticle is the 'o', make sure your projectiles vector is going to hit the '>' first. There have been some that SEEM unhittable, and just require you to line it up better.
Also, pay attention to the tiny dot I side the SRV reticle, that needs to line up with a certain part of the object too.
But there are still some that simply cannot be hit, which is the real problem.