Two issues happening simultaneously, here.
First, it seems that when two Local Threats are present, destroying one of them can turn the other Local Threat into an inert illusion. It won't do anything and the player can't shoot it. However, the slot can still be occupied by a functioning Local Threat, making the text hard or impossible to read.
Second, with the Beam Splitter upgrade, I had accumulated 5 laser charges prior to the Mothership showing up (I'll explain how later because this is a different bug), so I clicked the Mothership 5 times in rapid succession. The Cargo Ship went from having +1 hitpoint to -4 hitpoints; it completely skipped zero.
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Separate from the screenshot above, it is possible to play more planets than technically allowed by repeatedly clicking various planets in-hand.