Ohh I missed the charge feature entirely, it was indeed the reason. Played to the point you get the ability again after my playthrough and the game certainly mentions it, I probably thought of that as a "cooldown" and pretty much ignored what it said. You should add a bar that shows the charge so that it's clearer.
With that I beat the game too, got the probe and killed the boss that was actually challenging as it seemed to expand infinitely and you had to escape it while shooting it and reload your torpedoes simultaneously. Not too impossible though, nice challenge. The probe had problems though, a couple of times it made the game lag horribly and had to quit. Quitting to the menu wasn't enough, because for some reason after loading the game the probe's FOV was broken and I couldn't reveal new areas with it. Activating the boss had another hitch since a couple of times it happened on its own when I got to the end of the passage, but after a few tries I had to destroy the probe to make it happen. One last problem I encountered was a crash on my second playthrough when I was fixing leak after getting the SC upgrade.
Good job on a very unique and fun game though, it was indeed me who couldn't figure out the dash!