And during this wait you can't scoop anything else. You just have to wait. But you can see if you can scoop something else or not because of the text on top of the scooping graphic. You have to wait for it to disappear.
When I first got back into ED, a couple of months ago, I experienced exactly the same thing as the OP.
At the time I was flying my newly purchased Mandalay and I wondered if it just kind of sucked at scooping.
Fortunately, I also had collectors on my ship and, when they wouldn't deliver stuff either, I realised something else was amiss.
Also, since I was in the process of completing some engineering, I soon realised that the SRV had a similar issue... to the point where I wondered whether there was something I'd forgotten to do after extending my SRV's cargo scoop and targeting the item I wanted to collect.
Pretty certain it's all related to the "transaction server" issue.
Sometimes (most of the time) it isn't a problem at all but there have been times when I just can't collect anything.
Incidentally (and possibly related), I see a lot of people complaining about extended periods of frameshift travel but that's something I've never experienced yet.
Maybe that's just a result of me playing at antisocial times, when there's not much load on the servers?