I've got that terrible sinking feeling right about now.
I was making a new fixture plate for my mill. Basically it's a 1" thick piece of aluminum that is 1/4" narrower than the machine limits, so I cut at the X-Y limits using a 1/2" end mill. This provides a nice sacrificial work surface and also gives me a visual of my usable workspace.
Well I carefully measured my tool lengths, set the Z-zero on the table, checked the tram and ensured it was perfectly flat everywhere. Checked my tool length, tightness, collet tightness, everything. Brought it down to .0005" from the table and it just skimmed some sharpie from the surface. Perfect. I made my program bottom level .003" so that it would not get close, and leave a small amount of flash that I could remove with a razor blade. I took light depths of cut in a helical 2D-contour program to minimize tool deflection.
And yet... someway, somehow, the tool managed to cut into the table on the finishing level. Only about .001", but STILL! HOW DID THIS HAPPEN!? Yes, the groove is outside of the usable working area and shallow, but it's still a blemish on my table I managed to keep perfect for 6 years. After kicking myself for the last 3 hours, I am still confused as to how this happened. Could spindle/tool temperature cause a .004" growth in tool Z height? I now have a constant reminder for the future, but unless I know what happened it can happen again.
Now... even though I am 99.9% not going to do anything about it, is there a way to fix this? Could I remove the table and have that top surface ground flat in the future? Like I said, it's only about .001" deep.