From Towbar wiki: "Mining will stop by default when cargo transfer done assuming you want to tow the ship into a station. To continue prime Towbar (Shift+N) and press mode (b), but this suggested only if you do not plan to tow the ship back to any dock. "
Plus you missed the "mining need to prime Towbar and press mode" message also when you have Ship Miner but in "Cargo only" mode. So you need chgange the mode with "b" key after you selected Towbar from the primable equipments with some Shift+N press.
Another wiki hint: Ship Miner Assistant.
Have a nice play!
a little help with the new game?
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