Could be server lag or it could be that you havent noticed them going into the R&D tab instead of your inventory. If they are not in your R&D tab then maybe submit a bug report.
Nitpicking is a time-honored tradition of science fiction. Asking your readers not to worry about the "little things" is like asking a dog not to sniff at people's crotches. If there's something that appears to violate natural laws, then you can expect someone's going to point it out. That's just the way things are.
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Still waiting to be able to use forum titles
They're going into your inventory because the intermediary 'material boxes' do not auto-unpack properly.
Convert your materials 50 at a time instead of 100 at a time to prevent this from happening.
Joined January 2009