not a bug as such, but if I have say 40 Files and I spend them on a production upgrade, the Folders become hidden again (and the same happens with each producer and its successor). it makes sense, but looks a little wonky when it happens.
I don't see how it affects you clicking the relics.
It only appears while yours mouse resides on the laser. If it leaves the laser the text disappears.
As i pointed in another answer: this is optional feature to make game more active. It's additional reward(you gain resources for each kill) and you don't miss much when upgrading ships :)
reload page for now. Thx for noticing, i'll take a look on all issues you posted. Click to collect is optional feature so don't worry about misses :)
Edit: weapon shop changed in new version.
Thanks for poiting it out, I will fix it with next patch!