This has been happening to me in space since earlier this week:
1. A yellow item marker appears.
2. I get near it and do "Take items".
3. I get a message that says my inventory is full.
4. I check my inventory, and yep, it's full.
5. I clear some space in my inventory by selling some junk (batteries, usually) to my replicator.
6. I once again do "Take items" but nothing happens. The item list appears, but clicking on "Take all" doesn't do anything, the item remains there, I get no error message, nothing.
Note that this only occurs if I try to take an item in space when my inventory is full to begin with. I am not sure at this time whether or not it happens on the ground. I do not recall this being a problem for me earlier than this week.
Just chiming in that I've had similar trouble even with free inventory space. The Take All button just doesn't seem to work sometimes, and it's definitely a new bug as of the March 3rd patch or thereabouts.
This is a new bug. It has happened to me several times with only a few things in inventory, but only in the last few days. I have tried everything to put the items into inventory with no luck. Then the next item might work fine.