So there's a "silent" check happening at the Ranch that gives you resources, to stop the manipulation of those resources - essentially the same check which happens when you teleport to the Base Camp.
However, because it's "silent" and you don't get a game message, if you then go to Base Camp you're only seeing how many resources you received since you last visited the ranch not since you last visited the Base Camp... which in turn makes it seem like you've received less than you should.
We've got a job to add similar messaging when you teleport to the Ranch so this should no longer be an issue when that goes out.
If however you do think you're experiencing a bug and have definitely not received any of the resources you should have since buying the pens, send me over your RSN and a bug report. Please and thank you :)