I see 5 waypoints for KDF. Were you doing anything weird while mining? Canceling the mini-game? Walking away while the laser is active?
I had a bug where I mined 5 on my KDF, but only 4 counted. I think I accidnetally clicked the X on the window to claim the Data Sample I got, and that's why it didn't count. Also, the loot box could not be reaccessed, like the scanning minigame loot boxes are if you accidentally click out of them.
In regards to KDF getting the 4/5 nodes. I experienced that as well. In the airlock, after i shot and killed the suits and Ferengi, very zombie like animations for suits. I went outsde to my 5 waypoints. I mined them all, but only 4 counted. I hopped around entire rock checking them. I went back to space disappointed, and wanted to restart, however It is not able to be dropped or completed.