Posting this here in case it helps with the issue, if you examine the screenshot you will see I have my scoop down, I have targeted the mat, in this case nickel, I have capacity as I only have 291 of 300, but as soon as I target the mat the message "material acquired" immediately pops up before you have a chance to grab it, you can then drive over the mat which will vanish as if it's scooped, but it never gets added to the inventory, I tried with about 6 lots of nicked and it just sat at 291.
I tried both geo and bio mats and different types of mats, they all behaved the same.