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Picking them by hand resets the spawn point properly, the autocrafter is probably grabbing them without properly resetting the spawner so it never regrows. I doubt it's intentional.
Whenever an algae is picked up, another starts to grow at a random position around the grower. Since you can't place the crafter and grower onto each other, there will be always a zone that is unreachable and all grown algae will end up there.
UPDATE: Followed a suggestion earlier in this thread about using the T1 algae grower. Built a "pier" 3-4 foundations long stretching out over lake but close to water, build 3 T1 algae growers around the end, put the autocrafter on the foundation in the center of this cluster. 3 foundations long allows autocrafter range to include 1 or more ore extractors at the shoreline. Algae is indeed harvested, a lot of it is produced, and at this point I'm autocrafting so much of the different things I need I haven't had to go harvest algae by hand in a while. Works great.
1. Save Game
2. Quit Game.
3. Reenter Game.
All your algae will be picked up by your Auto-Crafter again. In fact, since the Auto-Crafter doesn't wait for the Algae to reach 100% maturity, your Auto-Crafter will immediately start processing all the Algae. And yes, you can quickly quit the game and reenter over and over again to process a ton of Algae very quickly (though that'd be a pretty lame way to play the game). I built an Algae farm with enough resources so that I don't have to think about closing and reopening the game. All my crafting of Bacteria Samples, Fertilizer, and Fertilizer T2 occur when I open my game and that's enough for my needs. I imagine this has happened to many people without them noticing and is likely why the responses to this thread seem inconsistent.
I believe that since the Auto-Crafter pulls the Algae before it reaches maturity, this somehow leaves behind an algae spawn point that is no longer able to grow. And since many of these spawn points still exist, the algae generator determines that it doesn't need to spawn any more algae spawn points. So basically, every time your Auto-Crafter pulls an algae, it leaves behind a dead algae spawn. Quitting and reentering the game deletes all of these dead algae spawns, and so the algae generator creates a bunch of new good algae spawns as you enter the game. This is why reentering the game works.
#1. Don't use Auto-crafters. Move them out of range.
#2. Use your drones. Place a locker near the autocrafter and have it demand algae.
Enjoy.