It sounds like your crops haven't finished growing to 100%. If they haven't you can harvest manually like you describe.
You can also increase the priority for "plant cut" , that's the job they do when harvesting things that you marked for cutting. If you only prioritise growing and the plant isn't fully grown, they will not auto-harvest it, even if it is marked for harvesting.
People don't research if there is anything else they can do (with normal priorities). Maybe you had a forbidden zone, locked door, or something else. But I don't think it's the game.
You can also increase the priority for "plant cut" , that's the job they do when harvesting things that you marked for cutting. If you only prioritise growing and the plant isn't fully grown, they will not auto-harvest it, even if it is marked for harvesting.
People don't research if there is anything else they can do (with normal priorities). Maybe you had a forbidden zone, locked door, or something else. But I don't think it's the game.