They complained, because unless you had a permit, you couldn't complete the mission. It was an oversight initially, which then led to complaints, and eventually the removal of any and all missions to systems requiring permit access.
Yeah it was particularly annoying with chained missions where a consecutive step would require you to travel to a permit locked system. Bad design, but the sledgehammer fix by removing permit locked systems from the mission generation was equally bad. I hope this will be fixed in the future.