I did a mining mission and it worked fine. When I finished a second mission and turned it in, I noticed that the crates were not removed from the ship's storage.
Then I selected a third mission and it gave me the mission accepted pop-up box, but also the mission complete box since I had the required boxes in storage.
So, for some reason with this new build of combining mining and combat, the mining mission code for removing crates from ship storage is either missing or not working.
I did try logging out and back in to see if this fixed the problem. It didn't. The I travelled to a different location, accepted a new mining mission and still the crates are not being removed.
I've stopped accepting missions now, but I'm also "stuck" with a bunch of crates in my storage and unable to run new missions. (Well...I can "run" them...but it would be cheating.)