When you have a weapon group, say Cannon/Cannon/Pulse, and you remove the three computers simultaneously with build area, the core will have a ghost connection to where the secondary cannon computer and pulse computer were. The connection can only be removed by selecting the core ("C") and placing the respective computer in that position, which causes the connection to disappear. Placing another type of computer does not remove the ghost connection, creating an additional connection from the core to this new computer.

Another issue caused by this bug, is that pasting weapon groups will yield a "overlapping modules, skipping some connections" message even without overlappings, and will not connect primary computers to any secondary or tertiary computers despite them being connected in the paste template.