Seems like the whole Mudd's Store thing has become a transporter malfunction. They should have led with 'Don't buy anything unless it's RIDICULOUSLY on sale.' Get it? Harry Mudd? He's a villain? He's trying to rip you off? Every item will eventually be hugely on sale so just wait for it? A mediocre idea, poorly executed.…
I'm getting this issue also, on Tier 2 ships. Only with my newly created toon though. If I bring in the same ship on an established toon I can equip it fully without issue. It's going to be annoying to try to level up missing weapons and consoles on my ship.