I'm beginning to be suspicious that the main quest did not go through testing. There are several sequences that need lander upgrades that you don't have access to:
1. Mercury and Io for radioactives. In the original game, both places were toxic, but it was possible to sneak your lander, get the stuff, and go.
2. Lacaille - NONE of the planets are landable with Degenerate Matter.
By the way, the first officer tells you that the planet is not lander friendly AFTER you lose your lander in a couple of instances. This should be prioritized for a fix.
I posted about the achievement issues in the support for low priority, but these should be high priority.