I second this issue - for me, on landing and collecting my first material, when I go to get a second material it just says "Material Acquired" when the cargo scoop is deployed. It is then like the cargo scoop is not deployed, and the material is kicked away if I get too close with the wheels or it disappears entirely. I have checked the health of my scoop and haven't seen this behaviour before. This has happened since the update...
I spent 4 days flying around the crystal spike sites filling up with mats a couple of weeks ago, and while there were some issues even then with collecting, as long as you had your scoop down it picked up every time, I never lost a single mat, but now yes this is entirely different. I see they reworked some stuff with the mats collecting in the patch so I suspect they broke something during that process.