How to reproduce this: 1) Go to a sundy or a terminal and activate it. 2) Click 'Resupply', and at the same moment (or just right after) click the button for your repair tool then your weapon. 3) You should now see that your repair tool has been replaced by your currently equipped weapon. I tried this a dozen times and it works pretty much 90 % of the time. Here's an image for reference:
