I have opened the large create by repairing the control panel but I cannot pick up the smaller crate inside. This is the same for every crate in the sector.
I was having the same problem myself. Was inside the wreck and had found two containers to collect, the first one was picked up just fine but the second one took a few tries to finally collect. The one that I was having a hard time picking up I was finally able to collect it after flying through the crate at various angles .
The wreck I found was pretty neat too. After I fixed the panel a hatch opened up and I was able to enter inside the wreckage and travel down a corridor to two separate sealed rooms that were also sealed.
Fair warning to anyone messing around with those wrecks, I would advise parking the ship outside of the wrecks gravity field. If you don't your going to have some serious trouble getting back into your ship as it constantly flips between the wrecks grav field and your ships own.