While completing the Crystal Mine storyline solo, I ran into an issue after defeating the crab boss and trying to interect with the valve in District 2.
The only possible way to “fix” my issue was swapping from Mouse mode, into Keyboard mode, then interacting with the Space bar. I was otherwise unable to click on the pipe on the wall.
i can confirm this, had the same problem.
just ran into the same issue here, I didn’t try to change the control mode tho, glad to see a solution
Had the same problem
Still having the issue… I use joypad mode, and switching modes isn’t helping me, I tried them all. I can’t finish the quest. 
Edit: I abandoned the quest, and killed the boss again. It worked. 
I was able to complete the quest with mouse mode, but using very fine tuning. There’s a blue patch of mineral on the ground near the pump–not at all near the valve as far as the mouse pointer is concerned. Slowly search the area by hovering the mouse until a speech bubble pops up.
It looks like the anchor for the pump is limited to a very small spot on the ground. The anchor should be a bit to the left and up to match the valve.
I had exactly the same issue and could solve it with exactly the same solution
I had this problem recently when i switched to Mouse over from Keyboard. This is most obvious in Goddess Ancient Garden map. Where we need to mind control the monsters while attacking them. Mouse will only attack and never mind-control.
Can they something like a space-bar (enter) in mouse mode?