Bug reports are coming in thick and fast, lol. I'm a solo dev on a shoestring budget, so it's to be expected I guess. In any case, I'm squashing them as fast as possible. Here's the latest list of changes/corrections:
When filling a system with crew members, the number of pips was being incorrectly calculated, especially in regards to "overfilling" the system (such as overfilling shields to negate damage for the next turn). This should be fixed now.
A number of edge cases has popped up in the tutorial which prevented progress or interacted weirdly. I think I've solved most, if not all, of these.
Game sometimes crashed if projectiles continued firing after an enemy had died. This should be fixed now.
Enemy AI for filling systems has been improved. It shouldn't spam fill system health so much now. More improvements will come later.
You can now clear your save file by going to the Options screen and pressing Ctrl + Shift + R. You should hear a mechanical sound play if it was successful. I recommend doing so before making much progress, as some of the prior bugs could have affected the save file.
Crew members were automatically ranked up to level 3 in all stats incorrectly. This has been reverted. Recommend cleaning the save file if this occurred during a playthrough.
Player and enemy have been made invincible for sections of the tutorial, in order to not have chaotic interactions. If invincibility doesn't end for some reason, firstly open the Escape menu by pressing Escape, and check the Tutorial Review. Make sure you've completed the last action on the list, as the game might be waiting for you to do something in order to progress. If you are sure you have, then please file a bug report.
Drawing of shield pips being wrong in some edge-cases has been corrected.
Max experience required for crew to level up has been increased.