The workshop is infinite storage though (unless the game mechanics are weird and decide to lock you out of getting more stuff every day)? It's the virtual resources that are capped unless you make more, well, storage. Either from industrial plots or containers. And it makes sense, if you haul enough junk to fill up a carrier, back to your settlement, it has to either clutter everything, be thrown away or be put somewhere, other than the very small workbench that magically holds it all.
Did you update to the christmas hotifx? I feel like that should solve it. Unless you salvaged something that had a million glass in it and there was a lot of free storage available. Then that's to be expected, if not in such numbers.