I'm having a similar problem too. I only have the one buggy. I left some items in the buggy storage (I can't remember precisely what) but it consisted of some plant and root seeds. I came back at a later date and the buggy had 3 stacks of 6 root seeds and 3 stacks of 6 plant seeds taking up the entirety of the displayed space. I thought that was a little odd and not quite how I left them in there, but I chalked it up to mis-remembering.
Tonight, I had an RTG, battery, comms tower, some radioactive ore, and root/grass seeds in my buggy before I had to save and quit to come back in a bit. After re-loading my save, I had 288 plant seeds, 288 root seeds, 52 radioactive ore, 10 batteries, 10 RTGs and 5 comms towers spread into more than the 6 stacks that display in the buggy storage.
I'll also send you my save folder, and I'll try to precisely re-duplicate the issue if I can.